Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T97982 | Target Info | |||
| Target Name | HUMAN cyclophilin D (CYP3) | ||||
| Synonyms | Peptidylprolyl cistrans isomerase F, mitochondrial; Peptidyl-prolyl cis-trans isomerase F, mitochondrial; PPIase F; Mitochondrial cyclophilin; Cyclophilin F; CyPM; CyP-M; CyP-D; CYP3 | ||||
| Gene Name | PPIF | ||||
| Biochemical Class | Cis-trans-isomerase | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: Dimethylformamide | Ligand Info | |||||
| Structure Description | Human cyclophilin D complexed with dimethylformamide | PDB:3RCG | ||||
| Method | X-ray diffraction | Resolution | 0.97 Å | Mutation | Yes | [1] |
| PDB Sequence |
GNPLVYLDVD
53 ANGKPLGRVV63 LELKADVVPK73 TAENFRALCT83 GEKGFGYKGS93 TFHRVIPSFM 103 CQAGDFTNHN113 GTGGKSIYGS123 RFPDENFTLK133 HVGPGVLSMA143 NAGPNTNGSQ 153 FFICTIKTDW163 LDGKHVVFGH173 VIEGMDVVKK183 IESFGSKSGR193 TSKKIVITDC 203 GQLS
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| Ligand Name: Carzenide | Ligand Info | |||||
| Structure Description | Human Cyclophilin D Complexed with a Fragment | PDB:3R4G | ||||
| Method | X-ray diffraction | Resolution | 1.05 Å | Mutation | Yes | [1] |
| PDB Sequence |
GNPLVYLDVD
53 ANGKPLGRVV63 LELKADVVPK73 TAENFRALCT83 GEKGFGYKGS93 TFHRVIPSFM 103 CQAGDFTNHN113 GTGGKSIYGS123 RFPDENFTLK133 HVGPGVLSMA143 NAGPNTNGSQ 153 FFICTIKTDW163 LDGKHVVFGH173 VIEGMDVVKK183 IESFGSKSGR193 TSKKIVITDC 203 GQLS
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| Ligand Name: 1313212-89-3 | Ligand Info | |||||
| Structure Description | Human Cyclophilin D Complexed with an Inhibitor at room temperature | PDB:4ZSC | ||||
| Method | X-ray diffraction | Resolution | 1.50 Å | Mutation | Yes | [2] |
| PDB Sequence |
GNPLVYLDVD
53 ANGKPLGRVV63 LELKADVVPK73 TAENFRALCT83 GEKGFGYKGS93 TFHRVIPSFM 103 CQAGDFTNHN113 GTGGKSIYGS123 RFPDENFTLK133 HVGPGVLSMA143 NAGPNTNGSQ 153 FFICTIKTDW163 LDGKHVVFGH173 VIEGMDVVKK183 IESFGSKSGR193 TSKKIVITDC 203 GQLS
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .EA4 or .EA42 or .EA43 or :3EA4;style chemicals stick;color identity;select .A:97 or .A:102 or .A:103 or .A:105 or .A:114 or .A:115 or .A:116 or .A:124 or .A:143 or .A:144 or .A:145 or .A:149 or .A:150 or .A:151 or .A:152 or .A:153 or .A:155 or .A:164 or .A:168; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 5-Amino-3-methylisoxazole | Ligand Info | |||||
| Structure Description | Human Cyclophilin D Complexed with a Fragment | PDB:3RDA | ||||
| Method | X-ray diffraction | Resolution | 1.07 Å | Mutation | Yes | [1] |
| PDB Sequence |
GNPLVYLDVD
53 ANGKPLGRVV63 LELKADVVPK73 TAENFRALCT83 GEKGFGYKGS93 TFHRVIPSFM 103 CQAGDFTNHN113 GTGGKSIYGS123 RFPDENFTLK133 HVGPGVLSMA143 NAGPNTNGSQ 153 FFICTIKTDW163 LDGKHVVFGH173 VIEGMDVVKK183 IESFGSKSGR193 TSKKIVITDC 203 GQLS
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .MIO or .MIO2 or .MIO3 or :3MIO;style chemicals stick;color identity;select .X:44 or .X:45 or .X:46 or .X:68 or .X:69 or .X:82 or .X:83 or .X:84 or .X:85 or .X:87 or .X:88 or .X:89 or .X:90 or .X:91 or .X:97 or .X:99 or .X:100 or .X:101 or .X:102 or .X:103 or .X:105 or .X:114 or .X:115 or .X:116 or .X:124 or .X:143 or .X:144 or .X:145 or .X:146 or .X:149 or .X:153 or .X:155 or .X:159 or .X:163 or .X:164 or .X:168 or .X:190 or .X:203; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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GLY44
3.308
ASN45
3.166
PRO46
3.871
ALA68
3.563
ASP69
4.544
CYS82
3.100
THR83
3.316
GLY84
2.902
GLU85
4.819
GLY87
3.326
PHE88
3.207
GLY89
3.223
TYR90
4.604
LYS91
3.423
ARG97
2.882
ILE99
3.823
PRO100
4.889
SER101
3.969
PHE102
3.244
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| Ligand Name: 1-(3-Aminophenyl)ethanone | Ligand Info | |||||
| Structure Description | Human Cyclophilin D Complexed with a Fragment | PDB:3R59 | ||||
| Method | X-ray diffraction | Resolution | 1.10 Å | Mutation | Yes | [1] |
| PDB Sequence |
GNPLVYLDVD
53 ANGKPLGRVV63 LELKADVVPK73 TAENFRALCT83 GEKGFGYKGS93 TFHRVIPSFM 103 CQAGDFTNHN113 GTGGKSIYGS123 RFPDENFTLK133 HVGPGVLSMA143 NAGPNTNGSQ 153 FFICTIKTDW163 LDGKHVVFGH173 VIEGMDVVKK183 IESFGSKSGR193 TSKKIVITDC 203 GQLS
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .3AO or .3AO2 or .3AO3 or :33AO;style chemicals stick;color identity;select .A:105 or .A:114 or .A:115 or .A:116 or .A:124 or .A:143 or .A:144 or .A:145 or .A:149 or .A:150 or .A:151 or .A:152 or .A:153; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: Sulfabenzamide | Ligand Info | |||||
| Structure Description | Human cyclophilin D complexed with N-[(4-aminophenyl)sulfonyl]benzamide | PDB:3RCF | ||||
| Method | X-ray diffraction | Resolution | 1.15 Å | Mutation | Yes | [1] |
| PDB Sequence |
GNPLVYLDVD
53 ANGKPLGRVV63 LELKADVVPK73 TAENFRALCT83 GEKGFGYKGS93 TFHRVIPSFM 103 CQAGDFTNHN113 GTGGKSIYGS123 RFPDENFTLK133 HVGPGVLSMA143 NAGPNTNGSQ 153 FFICTIKTDW163 LDGKHVVFGH173 VIEGMDVVKK183 IESFGSKSGR193 TSKKIVITDC 203 GQLS
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .BS4 or .BS42 or .BS43 or :3BS4;style chemicals stick;color identity;select .A:97 or .A:99 or .A:102 or .A:103 or .A:105 or .A:114 or .A:143 or .A:144 or .A:145 or .A:146 or .A:155 or .A:163 or .A:164 or .A:168; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 1-Formylpiperazine | Ligand Info | |||||
| Structure Description | Human Cyclophilin D Complexed with a Fragment | PDB:3RCK | ||||
| Method | X-ray diffraction | Resolution | 1.26 Å | Mutation | Yes | [1] |
| PDB Sequence |
GNPLVYLDVD
53 ANGKPLGRVV63 LELKADVVPK73 TAENFRALCT83 GEKGFGYKGS93 TFHRVIPSFM 103 CQAGDFTNHN113 GTGGKSIYGS123 RFPDENFTLK133 HVGPGVLSMA143 NAGPNTNGSQ 153 FFICTIKTDW163 LDGKHVVFGH173 VIEGMDVVKK183 IESFGSKSGR193 TSKKIVITDC 203 GQLS
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .1FP or .1FP2 or .1FP3 or :31FP;style chemicals stick;color identity;select .X:45 or .X:65 or .X:67 or .X:69 or .X:70 or .X:96 or .X:97 or .X:99 or .X:100 or .X:101 or .X:102 or .X:103 or .X:105 or .X:113 or .X:114 or .X:115 or .X:116 or .X:124 or .X:132 or .X:142 or .X:143 or .X:144 or .X:145 or .X:149 or .X:150 or .X:151 or .X:152 or .X:153 or .X:155 or .X:159 or .X:163 or .X:164 or .X:168 or .X:173; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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ASN45
3.677
GLU65
3.923
LYS67
2.509
ASP69
2.737
VAL70
3.799
HIS96
3.330
ARG97
3.447
ILE99
4.531
PRO100
3.936
SER101
3.038
PHE102
3.644
MET103
3.046
GLN105
2.751
ASN113
4.241
GLY114
3.140
THR115
3.537
GLY116
3.752
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| Ligand Name: 1-Formylpyrrolidine | Ligand Info | |||||
| Structure Description | Human Cyclophilin D Complexed with a Fragment | PDB:3R54 | ||||
| Method | X-ray diffraction | Resolution | 1.35 Å | Mutation | Yes | [1] |
| PDB Sequence |
GNPLVYLDVD
53 ANGKPLGRVV63 LELKADVVPK73 TAENFRALCT83 GEKGFGYKGS93 TFHRVIPSFM 103 CQAGDFTNHN113 GTGGKSIYGS123 RFPDENFTLK133 HVGPGVLSMA143 NAGPNTNGSQ 153 FFICTIKTDW163 LDGKHVVFGH173 VIEGMDVVKK183 IESFGSKSGR193 TSKKIVITDC 203 GQLS
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .FP6 or .FP62 or .FP63 or :3FP6;style chemicals stick;color identity;select .A:97 or .A:102 or .A:103 or .A:105 or .A:143 or .A:144 or .A:155 or .A:164 or .A:168; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 1H-Indazol-6-amine | Ligand Info | |||||
| Structure Description | Human Cyclophilin D Complexed with a Fragment | PDB:3R56 | ||||
| Method | X-ray diffraction | Resolution | 1.40 Å | Mutation | Yes | [1] |
| PDB Sequence |
GNPLVYLDVD
53 ANGKPLGRVV63 LELKADVVPK73 TAENFRALCT83 GEKGFGYKGS93 TFHRVIPSFM 103 CQAGDFTNHN113 GTGGKSIYGS123 RFPDENFTLK133 HVGPGVLSMA143 NAGPNTNGSQ 153 FFICTIKTDW163 LDGKHVVFGH173 VIEGMDVVKK183 IESFGSKSGR193 TSKKIVITDC 203 GQLS
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .6AI or .6AI2 or .6AI3 or :36AI;style chemicals stick;color identity;select .A:105 or .A:114 or .A:115 or .A:116 or .A:124 or .A:143 or .A:144 or .A:145 or .A:149 or .A:150 or .A:151 or .A:152 or .A:153; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 3,6,9,12,15,18-Hexaoxaicosane-1,20-diol | Ligand Info | |||||
| Structure Description | Human Cyclophilin D Complexed with a Fragment | PDB:3R56 | ||||
| Method | X-ray diffraction | Resolution | 1.40 Å | Mutation | Yes | [1] |
| PDB Sequence |
GNPLVYLDVD
53 ANGKPLGRVV63 LELKADVVPK73 TAENFRALCT83 GEKGFGYKGS93 TFHRVIPSFM 103 CQAGDFTNHN113 GTGGKSIYGS123 RFPDENFTLK133 HVGPGVLSMA143 NAGPNTNGSQ 153 FFICTIKTDW163 LDGKHVVFGH173 VIEGMDVVKK183 IESFGSKSGR193 TSKKIVITDC 203 GQLS
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .P33 or .P332 or .P333 or :3P33;style chemicals stick;color identity;select .A:135 or .A:136 or .A:137 or .A:138 or .A:139 or .A:173; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 3-(3-Methyl-5-oxo-4,5-dihydro-1H-pyrazol-1-yl)benzenesulfonamide | Ligand Info | |||||
| Structure Description | Human Cyclophilin D Complexed with a Fragment | PDB:3RD9 | ||||
| Method | X-ray diffraction | Resolution | 1.40 Å | Mutation | Yes | [1] |
| PDB Sequence |
GNPLVYLDVD
53 ANGKPLGRVV63 LELKADVVPK73 TAENFRALCT83 GEKGFGYKGS93 TFHRVIPSFM 103 CQAGDFTNHN113 GTGGKSIYGS123 RFPDENFTLK133 HVGPGVLSMA143 NAGPNTNGSQ 153 FFICTIKTDW163 LDGKHVVFGH173 VIEGMDVVKK183 IESFGSKSGR193 TSKKIVITDC 203 GQLS
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .MSY or .MSY2 or .MSY3 or :3MSY;style chemicals stick;color identity;select .X:96 or .X:97 or .X:105 or .X:113 or .X:114 or .X:142 or .X:143 or .X:144 or .X:145 or .X:153 or .X:155 or .X:168; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 3-Amino-5-methylisoxazole | Ligand Info | |||||
| Structure Description | Human cyclophilin D complexed with 5-methyl-1,2-oxazol-3-amine | PDB:3RCI | ||||
| Method | X-ray diffraction | Resolution | 1.44 Å | Mutation | Yes | [1] |
| PDB Sequence |
GNPLVYLDVD
53 ANGKPLGRVV63 LELKADVVPK73 TAENFRALCT83 GEKGFGYKGS93 TFHRVIPSFM 103 CQAGDFTNHN113 GTGGKSIYGS123 RFPDENFTLK133 HVGPGVLSMA143 NAGPNTNGSQ 153 FFICTIKTDW163 LDGKHVVFGH173 VIEGMDVVKK183 IESFGSKSGR193 TSKKIVITDC 203 GQLS
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .M3I or .M3I2 or .M3I3 or :3M3I;style chemicals stick;color identity;select .X:96 or .X:97 or .X:102 or .X:103 or .X:105 or .X:113 or .X:114 or .X:116 or .X:124 or .X:135 or .X:136 or .X:137 or .X:138 or .X:139 or .X:142 or .X:143 or .X:144 or .X:145 or .X:149 or .X:151 or .X:153 or .X:155 or .X:164 or .X:168 or .X:173; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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HIS96
3.099
ARG97
3.582
PHE102
4.038
MET103
3.874
GLN105
2.871
ASN113
3.245
GLY114
3.332
GLY116
4.906
ARG124
2.993
VAL135
3.420
GLY136
3.542
PRO137
2.870
GLY138
4.755
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| Ligand Name: 3-(5-(Chloromethyl)-1,2,4-oxadiazol-3-yl)aniline | Ligand Info | |||||
| Structure Description | Human Cyclophilin D Complexed with a Fragment | PDB:3RDB | ||||
| Method | X-ray diffraction | Resolution | 1.55 Å | Mutation | Yes | [1] |
| PDB Sequence |
GNPLVYLDVD
53 ANGKPLGRVV63 LELKADVVPK73 TAENFRALCT83 GEKGFGYKGS93 TFHRVIPSFM 103 CQAGDFTNHN113 GTGGKSIYGS123 RFPDENFTLK133 HVGPGVLSMA143 NAGPNTNGSQ 153 FFICTIKTDW163 LDGKHVVFGH173 VIEGMDVVKK183 IESFGSKSGR193 TSKKIVITDC 203 GQLS
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .5MZ or .5MZ2 or .5MZ3 or :35MZ;style chemicals stick;color identity;select .A:105 or .A:114 or .A:115 or .A:116 or .A:124 or .A:143 or .A:144 or .A:145 or .A:149 or .A:150 or .A:151 or .A:152 or .A:153; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 3-(1,3-Oxazol-5-yl)aniline | Ligand Info | |||||
| Structure Description | Human Cyclophilin D Complexed with a Fragment | PDB:3RCL | ||||
| Method | X-ray diffraction | Resolution | 1.70 Å | Mutation | Yes | [1] |
| PDB Sequence |
GNPLVYLDVD
53 ANGKPLGRVV63 LELKADVVPK73 TAENFRALCT83 GEKGFGYKGS93 TFHRVIPSFM 103 CQAGDFTNHN113 GTGGKSIYGS123 RFPDENFTLK133 HVGPGVLSMA143 NAGPNTNGSQ 153 FFICTIKTDW163 LDGKHVVFGH173 VIEGMDVVKK183 IESFGSKSGR193 TSKKIVITDC 203 GQLS
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .5AO or .5AO2 or .5AO3 or :35AO;style chemicals stick;color identity;select .A:105 or .A:114 or .A:115 or .A:116 or .A:124 or .A:143 or .A:144 or .A:145 or .A:149 or .A:150 or .A:151 or .A:152 or .A:153; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: N-(3-Aminophenyl)acetamide | Ligand Info | |||||
| Structure Description | Human Cyclophilin D Complexed with a Fragment | PDB:3R57 | ||||
| Method | X-ray diffraction | Resolution | 1.71 Å | Mutation | Yes | [1] |
| PDB Sequence |
GNPLVYLDVD
53 ANGKPLGRVV63 LELKADVVPK73 TAENFRALCT83 GEKGFGYKGS93 TFHRVIPSFM 103 CQAGDFTNHN113 GTGGKSIYGS123 RFPDENFTLK133 HVGPGVLSMA143 NAGPNTNGSQ 153 FFICTIKTDW163 LDGKHVVFGH173 VIEGMDVVKK183 IESFGSKSGR193 TSKKIVITDC 203 GQLS
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .N3M or .N3M2 or .N3M3 or :3N3M;style chemicals stick;color identity;select .A:67 or .A:97 or .A:102 or .A:103 or .A:105 or .A:114 or .A:115 or .A:116 or .A:124 or .A:135 or .A:136 or .A:137 or .A:138 or .A:139 or .A:143 or .A:144 or .A:145 or .A:146 or .A:147 or .A:149 or .A:150 or .A:151 or .A:152 or .A:153 or .A:155 or .A:163 or .A:164 or .A:167 or .A:168 or .A:173 or .A:174; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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LYS67
4.074
ARG97
3.411
PHE102
3.568
MET103
3.774
GLN105
4.642
GLY114
3.285
THR115
3.397
GLY116
4.468
ARG124
2.826
VAL135
3.674
GLY136
4.439
PRO137
2.672
GLY138
3.341
VAL139
3.485
ALA143
3.707
ASN144
2.783
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| Ligand Name: 8-Aminoquinoline | Ligand Info | |||||
| Structure Description | Human cyclophilin D complexed with quinolin-8-amine | PDB:3R49 | ||||
| Method | X-ray diffraction | Resolution | 1.77 Å | Mutation | Yes | [1] |
| PDB Sequence |
GNPLVYLDVD
53 ANGKPLGRVV63 LELKADVVPK73 TAENFRALCT83 GEKGFGYKGS93 TFHRVIPSFM 103 CQAGDFTNHN113 GTGGKSIYGS123 RFPDENFTLK133 HVGPGVLSMA143 NAGPNTNGSQ 153 FFICTIKTDW163 LDGKHVVFGH173 VIEGMDVVKK183 IESFGSKSGR193 TSKKIVITDC 203 GQLS
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .Q8A or .Q8A2 or .Q8A3 or :3Q8A;style chemicals stick;color identity;select .A:105 or .A:114 or .A:115 or .A:116 or .A:124 or .A:135 or .A:137 or .A:138 or .A:139 or .A:143 or .A:144 or .A:145 or .A:149 or .A:150 or .A:151 or .A:153 or .A:173 or .A:174; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: N-[(5-ethyl-4-oxo-1,2,3,6-tetrahydro-1,5-benzodiazocin-8-yl)methyl]-7-methyl-2-oxo-1,3-dihydropyrazolo[1,5-a]pyrimidin-8-ium-6-carboxamide | Ligand Info | |||||
| Structure Description | Human Cyclophilin D in complex with N-[(5-ethyl-4-oxo-1,2,3,4,5,6- hexahydro-1,5-benzodiazocin-8-yl)methyl]-7-methyl-2-oxo-1H,2H-pyrazolo[1,5-a]pyrimidine-6-carboxamide | PDB:7PMT | ||||
| Method | X-ray diffraction | Resolution | 0.98 Å | Mutation | Yes | [3] |
| PDB Sequence |
GNPLVYLDVD
11 ANGKPLGRVV21 LELKADVVPK31 TAENFRALCT41 GEKGFGYKGS51 TFHRVIPSFM 61 CQAGDFTNHN71 GTGGKSIYGS81 RFPDENFTLK91 HVGPGVLSMA101 NAGPNTNGSQ 111 FFICTIKTDW121 LDGKHVVFGH131 VIEGMDVVKK141 IESFGSKSGR151 TSKKIVITDC 161 GQLS
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .7UO or .7UO2 or .7UO3 or :37UO;style chemicals stick;color identity;select .A:54 or .A:55 or .A:63 or .A:71 or .A:72 or .A:73 or .A:74 or .A:75 or .A:76 or .A:81 or .A:82 or .A:101 or .A:102 or .A:103 or .A:107 or .A:108 or .A:109 or .A:110 or .A:111 or .A:149 or .A:150; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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HIS54
2.924
ARG55
2.588
GLN63
2.710
ASN71
4.142
GLY72
2.588
THR73
3.312
GLY74
3.603
GLY75
3.995
LYS76
4.355
SER81
3.270
ARG82
1.872
|
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| Ligand Name: N-(5-ethyl-4-oxidanylidene-1,2,3,6-tetrahydro-1,5-benzodiazocin-8-yl)-7-methyl-2-oxidanylidene-1H-pyrazolo[1,5-a]pyrimidine-6-carboxamide | Ligand Info | |||||
| Structure Description | Human Cyclophilin D in complex with N-(5-ethyl-4-oxo-1,2,3,4,5,6-hexahydro-1,5-benzodiazocin-8-yl)-7methyl-2-oxo-1H,2H-pyrazolo[1,5-a]pyrimidine-6-carboxamide | PDB:7OGI | ||||
| Method | X-ray diffraction | Resolution | 1.01 Å | Mutation | Yes | [4] |
| PDB Sequence |
GNPLVYLDVD
11 ANGKPLGRVV21 LELKADVVPK31 TAENFRALCT41 GEKGFGYKGS51 TFHRVIPSFM 61 CQAGDFTNHN71 GTGGKSIYGS81 RFPDENFTLK91 HVGPGVLSMA101 NAGPNTNGSQ 111 FFICTIKTDW121 LDGKHVVFGH131 VIEGMDVVKK141 IESFGSKSGR151 TSKKIVITDC 161 GQLS
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .VDH or .VDH2 or .VDH3 or :3VDH;style chemicals stick;color identity;select .A:54 or .A:55 or .A:63 or .A:71 or .A:72 or .A:73 or .A:74 or .A:75 or .A:76 or .A:81 or .A:82 or .A:83 or .A:101 or .A:102 or .A:103 or .A:107 or .A:108 or .A:109 or .A:110 or .A:111 or .A:149 or .A:150; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
HIS54
2.117
ARG55
2.745
GLN63
2.512
ASN71
4.163
GLY72
2.391
THR73
2.687
GLY74
3.084
GLY75
3.925
LYS76
4.643
SER81
3.043
ARG82
2.163
|
|||||
| Ligand Name: Ethyl N-{[3-(Pyridin-4-Yl)benzyl]carbamoyl}glycinate | Ligand Info | |||||
| Structure Description | Human Cyclophilin D Complexed with Inhibitor. | PDB:5CBU | ||||
| Method | X-ray diffraction | Resolution | 1.40 Å | Mutation | Yes | [5] |
| PDB Sequence |
GNPLVYLDVD
11 ANGKPLGRVV21 LELKADVVPK31 TAENFRALCT41 GEKGFGYKGS51 TFHRVIPSFM 61 CQAGDFTNHN71 GTGGKSIYGS81 RFPDENFTLK91 HVGPGVLSMA101 NAGPNTNGSQ 111 FFICTIKTDW121 LDGKHVVFGH131 VIEGMDVVKK141 IESFGSKSGR151 TSKKIVITDC 161 GQLS
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .4ZM or .4ZM2 or .4ZM3 or :34ZM;style chemicals stick;color identity;select .A:13 or .A:52 or .A:53 or .A:54 or .A:55 or .A:60 or .A:61 or .A:63 or .A:70 or .A:71 or .A:72 or .A:81 or .A:82 or .A:100 or .A:101 or .A:102 or .A:103 or .A:107 or .A:108 or .A:109 or .A:111 or .A:113 or .A:122 or .A:126 or .A:149 or .A:150 or .A:151 or .A:152 or .A:153 or .A:154 or .A:155; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ASN13
4.091
THR52
3.532
PHE53
4.085
HIS54
3.186
ARG55
3.101
PHE60
3.836
MET61
3.880
GLN63
2.951
HIS70
2.919
ASN71
3.418
GLY72
3.285
SER81
3.778
ARG82
2.955
MET100
4.953
ALA101
3.220
ASN102
3.050
|
|||||
| Ligand Name: Ethyl N-(Benzylcarbamoyl)glycinate | Ligand Info | |||||
| Structure Description | Human Cyclophilin D Complexed with Inhibitor | PDB:5CBT | ||||
| Method | X-ray diffraction | Resolution | 1.45 Å | Mutation | No | [6] |
| PDB Sequence |
GNPLVYLDVD
11 ANGKPLGRVV21 LELKADVVPK31 TAENFRALCT41 GEKGFGYKGS51 TFHRVIPSFM 61 CQAGDFTNHN71 GTGGKSIYGS81 RFPDENFTLK91 HVGPGVLSMA101 NAGPNTNGSQ 111 FFICTIKTDW121 LDGKHVVFGH131 VIEGMDVVKK141 IESFGSKSGR151 TSKKIVITDC 161 GQLS
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .4ZL or .4ZL2 or .4ZL3 or :34ZL;style chemicals stick;color identity;select .A:55 or .A:60 or .A:61 or .A:63 or .A:72 or .A:73 or .A:74 or .A:100 or .A:101 or .A:102 or .A:103 or .A:107 or .A:111 or .A:113 or .A:122 or .A:126; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: (4S,7S,11R,13E,19S)-N-[2-(2-aminoethoxy)ethyl]-7-benzyl-4-[(3-methylphenyl)methyl]-3,6,12,15,21-pentaoxo-1,3,4,5,6,7,8,9,10,12,15,16,17,18,19,20,21,22-octadecahydro-2H-7,11-methano-2,5,11,16,20-benzopentaazacyclotetracosine-19-carboxamide | Ligand Info | |||||
| Structure Description | Structure of Cyclophilin D Peptidyl-Prolyl Isomerase Domain bound to Macrocyclic Inhibitor B3 | PDB:7TH1 | ||||
| Method | X-ray diffraction | Resolution | 1.52 Å | Mutation | Yes | [7] |
| PDB Sequence |
NANPLVYLDV
10 DANGKPLGRV20 VLELKADVVP30 KTAENFRALC40 TGEKGFGYKG50 STFHRVIPSF 60 MCQAGDFTNH70 NGTGGKSIYG80 SRFPDENFTL90 KHVGPGVLSM100 ANAGPNTNGS 110 QFFICTIKTD120 WLDGKHVVFG130 HVIEGMDVVK140 KIESFGSKSG150 RTSKKIVITD 160 CGQLS
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .I5J or .I5J2 or .I5J3 or :3I5J;style chemicals stick;color identity;select .X:54 or .X:55 or .X:57 or .X:58 or .X:59 or .X:60 or .X:61 or .X:63 or .X:71 or .X:72 or .X:73 or .X:74 or .X:82 or .X:101 or .X:102 or .X:103 or .X:107 or .X:108 or .X:109 or .X:110 or .X:111 or .X:112 or .X:113 or .X:117 or .X:121 or .X:122 or .X:126 or .X:148; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
HIS54
4.948
ARG55
1.900
ILE57
2.334
PRO58
2.522
SER59
2.356
PHE60
2.453
MET61
3.438
GLN63
2.334
ASN71
3.145
GLY72
2.100
THR73
2.567
GLY74
3.648
ARG82
2.225
ALA101
2.521
|
|||||
| Ligand Name: Ethyl N-{[3-(Pyridin-3-Yl)benzyl]carbamoyl}glycinate | Ligand Info | |||||
| Structure Description | Human Cyclophilin D Complexed with Inhibitor | PDB:5CBV | ||||
| Method | X-ray diffraction | Resolution | 1.80 Å | Mutation | Yes | [8] |
| PDB Sequence |
GNPLVYLDVD
11 ANGKPLGRVV21 LELKADVVPK31 TAENFRALCT41 GEKGFGYKGS51 TFHRVIPSFM 61 CQAGDFTNHN71 GTGGKSIYGS81 RFPDENFTLK91 HVGPGVLSMA101 NAGPNTNGSQ 111 FFICTIKTDW121 LDGKHVVFGH131 VIEGMDVVKK141 IESFGSKSGR151 TSKKIVITDC 161 GQLS
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .4ZP or .4ZP2 or .4ZP3 or :34ZP;style chemicals stick;color identity;select .A:55 or .A:60 or .A:61 or .A:63 or .A:72 or .A:73 or .A:74 or .A:82 or .A:101 or .A:102 or .A:103 or .A:107 or .A:109 or .A:111 or .A:113 or .A:122 or .A:126; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: Ethyl N-{[4-(Acetylamino)benzyl]carbamoyl}glycinate | Ligand Info | |||||
| Structure Description | Human Cyclophilin D Complexed with Inhibitor. | PDB:5CBW | ||||
| Method | X-ray diffraction | Resolution | 1.80 Å | Mutation | Yes | [9] |
| PDB Sequence |
GNPLVYLDVD
11 ANGKPLGRVV21 LELKADVVPK31 TAENFRALCT41 GEKGFGYKGS51 TFHRVIPSFM 61 CQAGDFTNHN71 GTGGKSIYGS81 RFPDENFTLK91 HVGPGVLSMA101 NAGPNTNGSQ 111 FFICTIKTDW121 LDGKHVVFGH131 VIEGMDVVKK141 IESFGSKSGR151 TSKKIVITDC 161 GQLS
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .4ZO or .4ZO2 or .4ZO3 or :34ZO;style chemicals stick;color identity;select .A:55 or .A:60 or .A:61 or .A:63 or .A:72 or .A:73 or .A:74 or .A:81 or .A:82 or .A:101 or .A:102 or .A:103 or .A:107 or .A:108 or .A:109 or .A:111 or .A:113 or .A:122 or .A:126; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: Ethyl N-[(4-Aminobenzyl)carbamoyl]-L-Methioninate | Ligand Info | |||||
| Structure Description | Human Cyclophilin D Complexed with Inhibitor | PDB:5CCR | ||||
| Method | X-ray diffraction | Resolution | 1.90 Å | Mutation | Yes | [10] |
| PDB Sequence |
GNPLVYLDVD
11 ANGKPLGRVV21 LELKADVVPK31 TAENFRALCT41 GEKGFGYKGS51 TFHRVIPSFM 61 CQAGDFTNHN71 GTGGKSIYGS81 RFPDENFTLK91 HVGPGVLSMA101 NAGPNTNGSQ 111 FFICTIKTDW121 LDGKHVVFGH131 VIEGMDVVKK141 IESFGSKSGR151 TSKKIVITDC 161 GQLS
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .4ZT or .4ZT2 or .4ZT3 or :34ZT;style chemicals stick;color identity;select .A:54 or .A:55 or .A:60 or .A:61 or .A:63 or .A:72 or .A:73 or .A:74 or .A:82 or .A:100 or .A:101 or .A:102 or .A:103 or .A:104 or .A:107 or .A:108 or .A:109 or .A:110 or .A:111 or .A:113 or .A:122 or .A:126; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
HIS54
4.962
ARG55
3.075
PHE60
3.879
MET61
3.889
GLN63
2.907
GLY72
3.096
THR73
4.344
GLY74
4.225
ARG82
3.248
MET100
4.967
ALA101
3.227
|
|||||
| Ligand Name: 1-(4-Aminobenzyl)-3-{2-Oxo-2-[(2r)-2-Phenylpyrrolidin-1-Yl]ethyl}urea | Ligand Info | |||||
| Structure Description | Human Cyclophilin D Complexed with Inhibitor | PDB:5CCS | ||||
| Method | X-ray diffraction | Resolution | 2.10 Å | Mutation | Yes | [11] |
| PDB Sequence |
GNPLVYLDVD
11 ANGKPLGRVV21 LELKADVVPK31 TAENFRALCT41 GEKGFGYKGS51 TFHRVIPSFM 61 CQAGDFTNHN71 GTGGKSIYGS81 RFPDENFTLK91 HVGPGVLSMA101 NAGPNTNGSQ 111 FFICTIKTDW121 LDGQHVVFGH131 VIEGMDVVKK141 IESFGSKSGR151 TSKKIVITDC 161 GQLS
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .C4Y or .C4Y2 or .C4Y3 or :3C4Y;style chemicals stick;color identity;select .X:55 or .X:60 or .X:61 or .X:63 or .X:72 or .X:73 or .X:74 or .X:82 or .X:100 or .X:101 or .X:102 or .X:103 or .X:107 or .X:108 or .X:109 or .X:110 or .X:111 or .X:113 or .X:122 or .X:126; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 4'-(((13S,4S,12S,E)-12-((2-(2-aminoethoxy)ethyl)carbamoyl)-13-benzyl-2,5,10,16,19-pentaoxo-3,6,11,15-tetraaza-1(3,1)-piperidina-8(1,2)-benzenacyclononadecaphan-17-en-4-yl)methyl)-2-methyl-[1,1'-biphenyl]-4-carboxylic acid | Ligand Info | |||||
| Structure Description | Structure of Cyclophilin D Peptidyl-Prolyl Isomerase Domain bound to Macrocyclic Inhibitor B21 | PDB:7TH6 | ||||
| Method | X-ray diffraction | Resolution | 0.97 Å | Mutation | Yes | [7] |
| PDB Sequence |
NPLVYLDVDA
54 NGKPLGRVVL64 ELKADVVPKT74 AENFRALCTG84 EKGFGYKGST94 FHRVIPSFMC 104 QAGDFTNHNG114 TGGKSIYGSR124 FPDENFTLKH134 VGPGVLSMAN144 AGPNTNGSQF 154 FICTIKTDWL164 DGKHVVFGHV174 IEGMDVVKKI184 ESFGSKSGRT194 SKKIVITDCG 204 QLS
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .I56 or .I562 or .I563 or :3I56;style chemicals stick;color identity;select .A:96 or .A:97 or .A:99 or .A:101 or .A:102 or .A:103 or .A:105 or .A:113 or .A:114 or .A:115 or .A:116 or .A:117 or .A:118 or .A:119 or .A:123 or .A:124 or .A:142 or .A:143 or .A:144 or .A:145 or .A:149 or .A:150 or .A:151 or .A:152 or .A:153 or .A:154 or .A:155 or .A:159 or .A:161 or .A:163 or .A:164 or .A:168 or .A:190; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
HIS96
4.170
ARG97
2.026
ILE99
4.142
SER101
2.849
PHE102
2.425
MET103
3.347
GLN105
2.140
ASN113
2.975
GLY114
2.046
THR115
2.224
GLY116
3.257
GLY117
3.254
LYS118
3.346
SER119
4.878
SER123
2.672
ARG124
2.468
MET142
4.962
|
|||||
| Ligand Name: 1-(4-Aminobenzyl)-3-{2-[(2r)-2-(2-Methoxyphenyl)pyrrolidin-1-Yl]-2-Oxoethyl}urea | Ligand Info | |||||
| Structure Description | Human Cyclophilin D Complexed with an Inhibitor | PDB:4J5E | ||||
| Method | X-ray diffraction | Resolution | 0.99 Å | Mutation | Yes | [1] |
| PDB Sequence |
GNPLVYLDVD
53 ANGKPLGRVV63 LELKADVVPK73 TAENFRALCT83 GEKGFGYKGS93 TFHRVIPSFM 103 CQAGDFTNHN113 GTGGKSIYGS123 RFPDENFTLK133 HVGPGVLSMA143 NAGPNTNGSQ 153 FFICTIKTDW163 LDGKHVVFGH173 VIEGMDVVKK183 IESFGSKSGR193 TSKKIVITDC 203 GQLS
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .7B7 or .7B72 or .7B73 or :37B7;style chemicals stick;color identity;select .X:97 or .X:99 or .X:102 or .X:103 or .X:105 or .X:114 or .X:115 or .X:116 or .X:124 or .X:142 or .X:143 or .X:144 or .X:145 or .X:149 or .X:150 or .X:151 or .X:152 or .X:153 or .X:155 or .X:163 or .X:164 or .X:168; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ARG97
2.069
ILE99
3.495
PHE102
3.076
MET103
2.945
GLN105
2.175
GLY114
3.287
THR115
3.755
GLY116
4.184
ARG124
3.466
MET142
4.975
ALA143
2.502
|
|||||
| Ligand Name: 1-(4-Aminobenzyl)-3-[(2s)-4-(Methylsulfanyl)-1-{(2r)-2-[2-(Methylsulfanyl)phenyl]pyrrolidin-1-Yl}-1-Oxobutan-2-Yl]urea | Ligand Info | |||||
| Structure Description | Human Cyclophilin D Complexed with an Inhibitor | PDB:4J5C | ||||
| Method | X-ray diffraction | Resolution | 1.03 Å | Mutation | Yes | [1] |
| PDB Sequence |
GNPLVYLDVD
53 ANGKPLGRVV63 LELKADVVPK73 TAENFRALCT83 GEKGFGYKGS93 TFHRVIPSFM 103 CQAGDFTNHN113 GTGGKSIYGS123 RFPDENFTLK133 HVGPGVLSMA143 NAGPNTNGSQ 153 FFICTIKTDW163 LDGKHVVFGH173 VIEGMDVVKK183 IESFGSKSGR193 TSKKIVITDC 203 GQLS
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .7I6 or .7I62 or .7I63 or :37I6;style chemicals stick;color identity;select .X:97 or .X:99 or .X:102 or .X:103 or .X:105 or .X:114 or .X:115 or .X:116 or .X:124 or .X:142 or .X:143 or .X:144 or .X:145 or .X:149 or .X:150 or .X:151 or .X:152 or .X:153 or .X:155 or .X:163 or .X:164 or .X:168; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ARG97
1.943
ILE99
3.500
PHE102
2.979
MET103
3.107
GLN105
2.170
GLY114
3.083
THR115
3.968
GLY116
4.267
ARG124
3.377
MET142
4.900
ALA143
2.566
|
|||||
| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: (4S,7S,11R,13E,19S)-N-[2-(2-aminoethoxy)ethyl]-7-benzyl-4-[(furan-2-yl)methyl]-3,6,12,15,21-pentaoxo-1,3,4,5,6,7,8,9,10,12,15,16,17,18,19,20,21,22-octadecahydro-2H-7,11-methano-2,5,11,16,20-benzopentaazacyclotetracosine-19-carboxamide | Ligand Info | |||||
| Structure Description | Structure of Cyclophilin D Peptidyl-Prolyl Isomerase Domain bound to Macrocyclic Inhibitor A26 | PDB:7TGT | ||||
| Method | X-ray diffraction | Resolution | 1.06 Å | Mutation | Yes | [7] |
| PDB Sequence |
ANPLVYLDVD
12 ANGKPLGRVV22 LELKADVVPK32 TAENFRALCT42 GEKGFGYKGS52 TFHRVIPSFM 62 CQAGDFTNHN72 GTGGKSIYGS82 RFPDENFTLK92 HVGPGVLSMA102 NAGPNTNGSQ 112 FFICTIKTDW122 LDGKHVVFGH132 VIEGMDVVKK142 IESFGSKSGR152 TSKKIVITDC 162 GQLS
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .I4F or .I4F2 or .I4F3 or :3I4F;style chemicals stick;color identity;select .X:55 or .X:56 or .X:58 or .X:59 or .X:60 or .X:61 or .X:62 or .X:64 or .X:72 or .X:73 or .X:74 or .X:75 or .X:83 or .X:102 or .X:103 or .X:104 or .X:108 or .X:109 or .X:110 or .X:111 or .X:112 or .X:113 or .X:114 or .X:118 or .X:120 or .X:122 or .X:123 or .X:127; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
HIS55
4.933
ARG56
1.995
ILE58
3.589
PRO59
4.949
SER60
3.144
PHE61
2.239
MET62
3.395
GLN64
2.321
ASN72
3.027
GLY73
2.147
THR74
2.791
GLY75
4.486
ARG83
3.147
ALA102
2.566
|
|||||
| Ligand Name: CypD-IN-4 | Ligand Info | |||||
| Structure Description | Structure of Cyclophilin D Peptidyl-Prolyl Isomerase Domain bound to Macrocyclic Inhibitor B53 | PDB:7THF | ||||
| Method | X-ray diffraction | Resolution | 1.10 Å | Mutation | Yes | [7] |
| PDB Sequence |
NPLVYLDVDA
54 NGKPLGRVVL64 ELKADVVPKT74 AENFRALCTG84 EKGFGYKGST94 FHRVIPSFMC 104 QAGDFTNHNG114 TGGKSIYGSR124 FPDENFTLKH134 VGPGVLSMAN144 AGPNTNGSQF 154 FICTIKTDWL164 DGKHVVFGHV174 IEGMDVVKKI184 ESFGSKSGRT194 SKKIVITDCG 204 QLS
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .I4R or .I4R2 or .I4R3 or :3I4R;style chemicals stick;color identity;select .A:96 or .A:97 or .A:99 or .A:102 or .A:103 or .A:105 or .A:113 or .A:114 or .A:115 or .A:116 or .A:117 or .A:118 or .A:119 or .A:121 or .A:122 or .A:123 or .A:124 or .A:125 or .A:142 or .A:143 or .A:144 or .A:145 or .A:149 or .A:150 or .A:151 or .A:152 or .A:153 or .A:154 or .A:155 or .A:163 or .A:164 or .A:168; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
HIS96
4.916
ARG97
1.931
ILE99
4.573
PHE102
2.800
MET103
3.355
GLN105
2.369
ASN113
2.770
GLY114
1.984
THR115
2.580
GLY116
2.772
GLY117
2.416
LYS118
2.229
SER119
1.983
TYR121
4.671
GLY122
4.126
SER123
2.479
|
|||||
| Ligand Name: (4S,7S,11R,13E,19S)-N-[2-(2-aminoethoxy)ethyl]-4-[(4-benzoylphenyl)methyl]-7-benzyl-3,6,12,15,21-pentaoxo-1,3,4,5,6,7,8,9,10,12,15,16,17,18,19,20,21,22-octadecahydro-2H-7,11-methano-2,5,11,16,20-benzopentaazacyclotetracosine-19-carboxamide | Ligand Info | |||||
| Structure Description | Structure of Cyclophilin D Peptidyl-Prolyl Isomerase Domain bound to Macrocyclic Inhibitor B1 | PDB:7TGU | ||||
| Method | X-ray diffraction | Resolution | 1.21 Å | Mutation | Yes | [7] |
| PDB Sequence |
ANPLVYLDVD
12 ANGKPLGRVV22 LELKADVVPK32 TAENFRALCT42 GEKGFGYKGS52 TFHRVIPSFM 62 CQAGDFTNHN72 GTGGKSIYGS82 RFPDENFTLK92 HVGPGVLSMA102 NAGPNTNGSQ 112 FFICTIKTDW122 LDGKHVVFGH132 VIEGMDVVKK142 IESFGSKSGR152 TSKKIVITDC 162 GQL
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .I44 or .I442 or .I443 or :3I44;style chemicals stick;color identity;select .X:55 or .X:56 or .X:58 or .X:59 or .X:60 or .X:61 or .X:62 or .X:64 or .X:72 or .X:73 or .X:74 or .X:75 or .X:76 or .X:77 or .X:82 or .X:83 or .X:102 or .X:103 or .X:104 or .X:105 or .X:108 or .X:109 or .X:110 or .X:111 or .X:112 or .X:113 or .X:114 or .X:118 or .X:122 or .X:123 or .X:127 or .X:149; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
HIS55
4.930
ARG56
1.973
ILE58
2.395
PRO59
2.132
SER60
2.338
PHE61
2.421
MET62
3.329
GLN64
2.320
ASN72
3.183
GLY73
2.117
THR74
2.680
GLY75
4.009
GLY76
4.192
LYS77
4.348
SER82
2.685
ARG83
2.509
|
|||||
| Ligand Name: 14-Ethyl-4,6-dioxa-10,14-diazatricyclo[7.6.0.0^{3,7}]pentadeca-1(9),2,7-trien-13-one | Ligand Info | |||||
| Structure Description | Human Cyclophilin D in complex with fragment | PDB:6R9U | ||||
| Method | X-ray diffraction | Resolution | 1.26 Å | Mutation | Yes | [12] |
| PDB Sequence |
GNPLVYLDVD
53 ANGKPLGRVV63 LELKADVVPK73 TAENFRALCT83 GEKGFGYKGS93 TFHRVIPSFM 103 CQAGDFTNHN113 GTGGKSIYGS123 RFPDENFTLK133 HVGPGVLSMA143 NAGPNTNGSQ 153 FFICTIKTDW163 LDGKHVVFGH173 VIEGMDVVKK183 IESFGSKSGR193 TSKKIVITDC 203 GQLS
|
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .JVQ or .JVQ2 or .JVQ3 or :3JVQ;style chemicals stick;color identity;select .A:105 or .A:114 or .A:115 or .A:116 or .A:117 or .A:118 or .A:123 or .A:124 or .A:143 or .A:144 or .A:145 or .A:149 or .A:150 or .A:151 or .A:153; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 1-(4-Aminobenzyl)-3-[2-Oxo-2-(Pyrrolidin-1-Yl)ethyl]urea | Ligand Info | |||||
| Structure Description | Human Cyclophilin D Complexed with an Inhibitor | PDB:4J58 | ||||
| Method | X-ray diffraction | Resolution | 1.28 Å | Mutation | Yes | [1] |
| PDB Sequence |
GNPLVYLDVD
53 ANGKPLGRVV63 LELKADVVPK73 TAENFRALCT83 GEKGFGYKGS93 TFHRVIPSFM 103 CQAGDFTNHN113 GTGGKSIYGS123 RFPDENFTLK133 HVGPGVLSMA143 NAGPNTNGSQ 153 FFICTIKTDW163 LDGKHVVFGH173 VIEGMDVVKK183 IESFGSKSGR193 TSKKIVITDC 203 GQLS
|
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .53Z or .53Z2 or .53Z3 or :353Z;style chemicals stick;color identity;select .A:97 or .A:102 or .A:103 or .A:105 or .A:114 or .A:115 or .A:116 or .A:124 or .A:142 or .A:143 or .A:144 or .A:145 or .A:149 or .A:150 or .A:151 or .A:152 or .A:153 or .A:155 or .A:164 or .A:168; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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ARG97
3.631
PHE102
3.332
MET103
3.592
GLN105
2.965
GLY114
3.311
THR115
3.930
GLY116
4.191
ARG124
3.396
MET142
4.854
ALA143
3.281
|
|||||
| Ligand Name: 1-(4-Aminobenzyl)-3-{2-[(2r)-2-(2-Bromophenyl)pyrrolidin-1-Yl]-2-Oxoethyl}urea | Ligand Info | |||||
| Structure Description | Human Cyclophilin D Complexed with an Inhibitor | PDB:4J5D | ||||
| Method | X-ray diffraction | Resolution | 1.32 Å | Mutation | Yes | [1] |
| PDB Sequence |
GNPLVYLDVD
53 ANGKPLGRVV63 LELKADVVPK73 TAENFRALCT83 GEKGFGYKGS93 TFHRVIPSFM 103 CQAGDFTNHN113 GTGGKSIYGS123 RFPDENFTLK133 HVGPGVLSMA143 NAGPNTNGSQ 153 FFICTIKTDW163 LDGKHVVFGH173 VIEGMDVVKK183 IESFGSKSGR193 TSKKIVITDC 203 GQLS
|
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .728 or .7282 or .7283 or :3728;style chemicals stick;color identity;select .X:97 or .X:99 or .X:102 or .X:103 or .X:105 or .X:114 or .X:115 or .X:116 or .X:124 or .X:143 or .X:144 or .X:145 or .X:149 or .X:150 or .X:151 or .X:152 or .X:153 or .X:155 or .X:163 or .X:164 or .X:168; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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ARG97
2.916
ILE99
3.998
PHE102
3.949
MET103
3.520
GLN105
2.962
GLY114
3.363
THR115
3.804
GLY116
4.033
ARG124
3.480
ALA143
3.254
ASN144
2.886
|
|||||
| Ligand Name: 1-(((2R,3S,6R)-3-hydroxy-2,3,4,6-tetrahydro-1H-2,6-methanobenzo[c][1,5]oxazocin-8-yl)methyl)-3-(2-((R)-2-(2-(methylthio)phenyl)pyrrolidin-1-yl)-2-oxoethyl)urea | Ligand Info | |||||
| Structure Description | Human Cyclophilin D in complex with 1-(((2R,3S,6R)-3-hydroxy-2,3,4,6-tetrahydro-1H-2,6-methanobenzo[c][1,5]oxazocin-8-yl)methyl)-3-(2-((R)-2-(2-(methylthio)phenyl)pyrrolidin-1-yl)-2-oxoethyl)urea | PDB:6R8O | ||||
| Method | X-ray diffraction | Resolution | 1.36 Å | Mutation | Yes | [12] |
| PDB Sequence |
GNPLVYLDVD
53 ANGKPLGRVV63 LELKADVVPK73 TAENFRALCT83 GEKGFGYKGS93 TFHRVIPSFM 103 CQAGDFTNHN113 GTGGKSIYGS123 RFPDENFTLK133 HVGPGVLSMA143 NAGPNTNGSQ 153 FFICTIKTDW163 LDGKHVVFGH173 VIEGMDVVKK183 IESFGSKSGR193 TSKKIVITDC 203 GQLS
|
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .JV2 or .JV22 or .JV23 or :3JV2;style chemicals stick;color identity;select .A:97 or .A:99 or .A:102 or .A:103 or .A:105 or .A:114 or .A:115 or .A:116 or .A:117 or .A:123 or .A:124 or .A:142 or .A:143 or .A:144 or .A:145 or .A:149 or .A:150 or .A:151 or .A:152 or .A:153 or .A:155 or .A:164 or .A:168; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ARG97
2.926
ILE99
4.022
PHE102
3.526
MET103
3.604
GLN105
2.970
GLY114
3.101
THR115
3.352
GLY116
3.584
GLY117
3.589
SER123
2.793
ARG124
3.599
MET142
4.979
|
|||||
| Ligand Name: 2-(exo-3,5-Dioxo-4-aza-tricyclo[5.2.1.02,6]dec-4-yl)-N-((1R,9R,10S)-10-hydroxy-12-oxa-8-aza-tricyclo[7.3.1.02,7]trideca-2(7),3,5-trien-4-ylmethyl)-acetamide | Ligand Info | |||||
| Structure Description | Human Cyclophilin D in complex with 2-(exo-3,5-Dioxo-4-aza-tricyclo[5.2.1.02,6]dec-4-yl)-N-((1R,9R,10S)-10-hydroxy-12-oxa-8-aza-tricyclo[7.3.1.02,7]trideca-2(7),3,5-trien-4-ylmethyl)-acetamide | PDB:6R8W | ||||
| Method | X-ray diffraction | Resolution | 1.40 Å | Mutation | Yes | [12] |
| PDB Sequence |
GNPLVYLDVD
53 ANGKPLGRVV63 LELKADVVPK73 TAENFRALCT83 GEKGFGYKGS93 TFHRVIPSFM 103 CQAGDFTNHN113 GTGGKSIYGS123 RFPDENFTLK133 HVGPGVLSMA143 NAGPNTNGSQ 153 FFICTIKTDW163 LDGKHVVFGH173 VIEGMDVVKK183 IESFGSKSGR193 TSKKIVITDC 203 GQLS
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .JVH or .JVH2 or .JVH3 or :3JVH;style chemicals stick;color identity;select .A:97 or .A:102 or .A:103 or .A:105 or .A:114 or .A:115 or .A:116 or .A:117 or .A:123 or .A:124 or .A:142 or .A:143 or .A:144 or .A:145 or .A:149 or .A:150 or .A:151 or .A:152 or .A:153 or .A:155 or .A:164 or .A:168; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ARG97
2.876
PHE102
3.608
MET103
3.924
GLN105
2.788
GLY114
3.137
THR115
3.460
GLY116
3.540
GLY117
3.702
SER123
3.049
ARG124
3.555
MET142
4.915
|
|||||
| Ligand Name: (4S,7S,11R,13E,19S)-N-[2-(2-aminoethoxy)ethyl]-7-benzyl-4-[([1,1'-biphenyl]-4-yl)methyl]-3,6,12,15,21-pentaoxo-1,3,4,5,6,7,8,9,10,12,15,16,17,18,19,20,21,22-octadecahydro-2H-7,11-methano-2,5,11,16,20-benzopentaazacyclotetracosine-19-carboxamide | Ligand Info | |||||
| Structure Description | Structure of Cyclophilin D Peptidyl-Prolyl Isomerase Domain bound to Macrocyclic Inhibitor B2 | PDB:7TGV | ||||
| Method | X-ray diffraction | Resolution | 1.46 Å | Mutation | Yes | [7] |
| PDB Sequence |
GNPLVYLDVD
11 ANGKPLGRVV21 LELKADVVPK31 TAENFRALCT41 GEKGFGYKGS51 TFHRVIPSFM 61 CQAGDFTNHN71 GTGGKSIYGS81 RFPDENFTLK91 HVGPGVLSMA101 NAGPNTNGSQ 111 FFICTIKTDW121 LDGKHVVFGH131 VIEGMDVVKK141 IESFGSKSGR151 TSKKIVITDC 161 GQLS
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .I3X or .I3X2 or .I3X3 or :3I3X;style chemicals stick;color identity;select .X:54 or .X:55 or .X:57 or .X:59 or .X:60 or .X:61 or .X:63 or .X:71 or .X:72 or .X:73 or .X:74 or .X:75 or .X:76 or .X:77 or .X:81 or .X:82 or .X:83 or .X:101 or .X:102 or .X:103 or .X:107 or .X:108 or .X:109 or .X:110 or .X:111 or .X:112 or .X:113 or .X:117 or .X:119 or .X:121 or .X:122 or .X:126; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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HIS54
4.326
ARG55
2.096
ILE57
3.930
SER59
3.610
PHE60
2.833
MET61
3.325
GLN63
2.344
ASN71
2.970
GLY72
2.124
THR73
2.759
GLY74
3.009
GLY75
2.957
LYS76
2.896
SER77
4.287
SER81
2.832
ARG82
2.542
|
|||||
| Ligand Name: 1-(4-Aminobenzyl)-3-{2-[(2r)-2-(2,5-Dimethoxyphenyl)pyrrolidin-1-Yl]-2-Oxoethyl}urea | Ligand Info | |||||
| Structure Description | Human Cyclophilin D Complexed with an Inhibitor | PDB:4J5A | ||||
| Method | X-ray diffraction | Resolution | 1.58 Å | Mutation | Yes | [13] |
| PDB Sequence |
GNPLVYLDVD
53 ANGKPLGRVV63 LELKADVVPK73 TAENFRALCT83 GEKGFGYKGS93 TFHRVIPSFM 103 CQAGDFTNHN113 GTGGKSIYGS123 RFPDENFTLK133 HVGPGVLSMA143 NAGPNTNGSQ 153 FFICTIKTDW163 LDGKHVVFGH173 VIEGMDVVKK183 IESFGSKSGR193 TSKKIVITDC 203 GQLS
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .67Z or .67Z2 or .67Z3 or :367Z;style chemicals stick;color identity;select .X:97 or .X:99 or .X:102 or .X:103 or .X:105 or .X:114 or .X:115 or .X:116 or .X:124 or .X:143 or .X:144 or .X:145 or .X:149 or .X:150 or .X:151 or .X:152 or .X:153 or .X:155 or .X:163 or .X:164 or .X:168; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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ARG97
2.916
ILE99
4.005
PHE102
3.635
MET103
3.499
GLN105
3.086
GLY114
3.259
THR115
4.033
GLY116
4.191
ARG124
3.352
ALA143
3.315
ASN144
2.842
|
|||||
| Ligand Name: 1-[2-[(2~{R})-2-(2-methylsulfanylphenyl)pyrrolidin-1-yl]-2-oxidanylidene-ethyl]-3-[[(1~{S},9~{S},10~{S})-10-oxidanyl-12-oxa-8-azatricyclo[7.3.1.0^{2,7}]trideca-2(7),3,5-trien-4-yl]methyl]urea | Ligand Info | |||||
| Structure Description | Human Cyclophilin D in complex with 1-((1S,9S,10S)-10-Hydroxy-12-oxa-8-aza-tricyclo[7.3.1.02,7]trideca-2,4,6-trien-4-ylmethyl)-3- {2-[(R)-2-(2-methylsulfanyl-phenyl)-pyrrolidin-1-yl]-2-oxo-ethyl}-urea | PDB:6R8L | ||||
| Method | X-ray diffraction | Resolution | 1.64 Å | Mutation | Yes | [12] |
| PDB Sequence |
GNPLVYLDVD
53 ANGKPLGRVV63 LELKADVVPK73 TAENFRALCT83 GEKGFGYKGS93 TFHRVIPSFM 103 CQAGDFTNHN113 GTGGKSIYGS123 RFPDENFTLK133 HVGPGVLSMA143 NAGPNTNGSQ 153 FFICTIKTDW163 LDGKHVVFGH173 VIEGMDVVKK183 IESFGSKSGR193 TSKKIVITDC 203 GQLS
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .JUZ or .JUZ2 or .JUZ3 or :3JUZ;style chemicals stick;color identity;select .A:97 or .A:99 or .A:102 or .A:103 or .A:105 or .A:114 or .A:115 or .A:116 or .A:117 or .A:118 or .A:123 or .A:124 or .A:143 or .A:144 or .A:145 or .A:149 or .A:150 or .A:151 or .A:152 or .A:153 or .A:155 or .A:164 or .A:168; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ARG97
3.001
ILE99
4.132
PHE102
3.467
MET103
3.559
GLN105
2.977
GLY114
3.060
THR115
3.356
GLY116
3.512
GLY117
3.284
LYS118
4.041
SER123
2.727
ARG124
4.411
|
|||||
| Ligand Name: N'-cyclopentyl-N-(pyridin-2-ylmethyl)oxamide | Ligand Info | |||||
| Structure Description | Human Cyclophilin D in complex with N-cyclopentyl-N'-pyridin-2-ylmethyl-oxalamide | PDB:6R9X | ||||
| Method | X-ray diffraction | Resolution | 1.66 Å | Mutation | Yes | [12] |
| PDB Sequence |
GNPLVYLDVD
53 ANGKPLGRVV63 LELKADVVPK73 TAENFRALCT83 GEKGFGYKGS93 TFHRVIPSFM 103 CQAGDFTNHN113 GTGGKSIYGS123 RFPDENFTLK133 HVGPGVLSMA143 NAGPNTNGSQ 153 FFICTIKTDW163 LDGKHVVFGH173 VIEGMDVVKK183 IESFGSKSGR193 TSKKIVITDC 203 GQLS
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .JW2 or .JW22 or .JW23 or :3JW2;style chemicals stick;color identity;select .A:97 or .A:102 or .A:103 or .A:105 or .A:114 or .A:115 or .A:116 or .A:143 or .A:144 or .A:145 or .A:153 or .A:155 or .A:164 or .A:168; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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||||||
| Ligand Name: (4S,7R,11S,13E,19S)-N-[2-(2-aminoethoxy)ethyl]-4-[(furan-2-yl)methyl]-3,6,12,15,21-pentaoxo-1,3,4,5,6,7,8,9,10,12,15,16,17,18,19,20,21,22-octadecahydro-2H-7,11-methano-2,5,11,16,20-benzopentaazacyclotetracosine-19-carboxamide | Ligand Info | |||||
| Structure Description | Structure of Cyclophilin D Peptidyl-Prolyl Isomerase Domain bound to Macrocyclic Inhibitor JOMBt | PDB:7TGS | ||||
| Method | X-ray diffraction | Resolution | 1.75 Å | Mutation | Yes | [7] |
| PDB Sequence |
GNPLVYLDVD
11 ANGKPLGRVV21 LELKADVVPK31 TAENFRALCT41 GEKGFGYKGS51 TFHRVIPSFM 61 CQAGDFTNHN71 GTGGKSIYGS81 RFPDENFTLK91 HVGPGVLSMA101 NAGPNTNGSQ 111 FFICTIKTDW121 LDGKHVVFGH131 VIEGMDVVKK141 IESFGSKSGR151 TSKKIVITDC 161 GQLS
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .I3Q or .I3Q2 or .I3Q3 or :3I3Q;style chemicals stick;color identity;select .X:54 or .X:55 or .X:57 or .X:60 or .X:61 or .X:63 or .X:71 or .X:72 or .X:73 or .X:74 or .X:82 or .X:100 or .X:101 or .X:102 or .X:103 or .X:107 or .X:108 or .X:109 or .X:111 or .X:112 or .X:113 or .X:121 or .X:122 or .X:126 or .X:148 or .X:149 or .X:150; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
HIS54
4.725
ARG55
1.885
ILE57
2.748
PHE60
2.656
MET61
3.637
GLN63
2.231
ASN71
3.587
GLY72
2.195
THR73
2.422
GLY74
4.383
ARG82
4.014
MET100
4.921
ALA101
2.380
ASN102
2.025
|
|||||
| Ligand Name: Ethyl N-{[(2-Aminopyridin-4-Yl)methyl]carbamoyl}glycinate | Ligand Info | |||||
| Structure Description | Human Cyclophilin D Complexed with Inhibitor | PDB:5CCQ | ||||
| Method | X-ray diffraction | Resolution | 1.80 Å | Mutation | Yes | [14] |
| PDB Sequence |
GNPLVYLDVD
11 ANGKPLGRVV21 LELKADVVPK31 TAENFRALCT41 GEKGFGYKGS51 TFHRVIPSFM 61 CQAGDFTNHN71 GTGGKSIYGS81 RFPDENFTLK91 HVGPGVLSMA101 NAGPNTNGSQ 111 FFICTIKTDW121 LDGKHVVFGH131 VIEGMDVVKK141 IESFGSKSGR151 TSKKIVITDC 161 GQLS
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .502 or .5022 or .5023 or :3502;style chemicals stick;color identity;select .A:55 or .A:60 or .A:61 or .A:63 or .A:72 or .A:73 or .A:74 or .A:100 or .A:101 or .A:102 or .A:103 or .A:107 or .A:111 or .A:113 or .A:122 or .A:126; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: Ethyl N-{[3-(3-Aminopyridin-4-Yl)benzyl]carbamoyl}glycinate | Ligand Info | |||||
| Structure Description | Human Cyclophilin D Complexed with Inhibitor | PDB:5CCN | ||||
| Method | X-ray diffraction | Resolution | 1.80 Å | Mutation | Yes | [15] |
| PDB Sequence |
GNPLVYLDVD
11 ANGKPLGRVV21 LELKADVVPK31 TAENFRALCT41 GEKGFGYKGS51 TFHRVIPSFM 61 CQAGDFTNHN71 GTGGKSIYGS81 RFPDENFTLK91 HVGPGVLSMA101 NAGPNTNGSQ 111 FFICTIKTDW121 LDGKHVVFGH131 VIEGMDVVKK141 IESFGSKSGR151 TSKKIVITDC 161 GQLS
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .4ZZ or .4ZZ2 or .4ZZ3 or :34ZZ;style chemicals stick;color identity;select .A:55 or .A:60 or .A:61 or .A:63 or .A:72 or .A:73 or .A:74 or .A:81 or .A:82 or .A:101 or .A:102 or .A:103 or .A:107 or .A:108 or .A:109 or .A:111 or .A:113 or .A:122 or .A:126; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 1-(4-Aminobenzyl)-3-{2-[(2r)-2-(Naphthalen-1-Yl)pyrrolidin-1-Yl]-2-Oxoethyl}urea | Ligand Info | |||||
| Structure Description | Human Cyclophilin D Complexed with an Inhibitor | PDB:4J59 | ||||
| Method | X-ray diffraction | Resolution | 1.92 Å | Mutation | Yes | [1] |
| PDB Sequence |
GNPLVYLDVD
53 ANGKPLGRVV63 LELKADVVPK73 TAENFRALCT83 GEKGFGYKGS93 TFHRVIPSFM 103 CQAGDFTNHN113 GTGGKSIYGS123 RFPDENFTLK133 HVGPGVLSMA143 NAGPNTNGSQ 153 FFICTIKTDW163 LDGKHVVFGH173 VIEGMDVVKK183 IESFGSKSGR193 TSKKIVITDC 203 GQLS
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .671 or .6712 or .6713 or :3671;style chemicals stick;color identity;select .A:97 or .A:99 or .A:102 or .A:103 or .A:105 or .A:114 or .A:115 or .A:116 or .A:124 or .A:143 or .A:144 or .A:145 or .A:149 or .A:150 or .A:151 or .A:152 or .A:153 or .A:155 or .A:163 or .A:164 or .A:168; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ARG97
3.113
ILE99
3.877
PHE102
3.616
MET103
3.402
GLN105
3.034
GLY114
3.335
THR115
3.799
GLY116
4.093
ARG124
3.495
ALA143
3.299
ASN144
2.883
|
|||||
| Ligand Name: (1~{R},9~{R},10~{S})-4-fluoranyl-12-oxa-8-azatricyclo[7.3.1.0^{2,7}]trideca-2(7),3,5-trien-10-ol | Ligand Info | |||||
| Structure Description | Human Cyclophilin D in complex with bicyclic fragment | PDB:6R9S | ||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | Yes | [12] |
| PDB Sequence |
GNPLVYLDVD
53 ANGKPLGRVV63 LELKADVVPK73 TAENFRALCT83 GEKGFGYKGS93 TFHRVIPSFM 103 CQAGDFTNHN113 GTGGKSIYGS123 RFPDENFTLK133 HVGPGVLSMA143 NAGPNTNGSQ 153 FFICTIKTDW163 LDGKHVVFGH173 VIEGMDVVKK183 IESFGSKSGR193 TSKKIVITDC 203 GQLS
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .JVN or .JVN2 or .JVN3 or :3JVN;style chemicals stick;color identity;select .A:105 or .A:114 or .A:115 or .A:116 or .A:117 or .A:123 or .A:124 or .A:143 or .A:144 or .A:145 or .A:149 or .A:150 or .A:151 or .A:152 or .A:153; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 2-[(1~{R},2~{R},6~{S},7~{S})-3,5-bis(oxidanylidene)-4-azatricyclo[5.2.1.0^{2,6}]decan-4-yl]ethanoic acid | Ligand Info | |||||
| Structure Description | Human Cyclophilin D in complex with norbornane fragment derivative | PDB:6RA1 | ||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | Yes | [12] |
| PDB Sequence |
GNPLVYLDVD
53 ANGKPLGRVV63 LELKADVVPK73 TAENFRALCT83 GEKGFGYKGS93 TFHRVIPSFM 103 CQAGDFTNHN113 GTGGKSIYGS123 RFPDENFTLK133 HVGPGVLSMA143 NAGPNTNGSQ 153 FFICTIKTDW163 LDGKHVVFGH173 VIEGMDVVKK183 IESFGSKSGR193 TSKKIVITDC 203 GQLS
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .JWB or .JWB2 or .JWB3 or :3JWB;style chemicals stick;color identity;select .A:97 or .A:102 or .A:103 or .A:105 or .A:114 or .A:142 or .A:143 or .A:144 or .A:153 or .A:155 or .A:164 or .A:168; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 1-(4-Aminobenzyl)-3-(2-{(2r)-2-[2-(Methylsulfanyl)phenyl]pyrrolidin-1-Yl}-2-Oxoethyl)urea | Ligand Info | |||||
| Structure Description | Human Cyclophilin D Complexed with an Inhibitor | PDB:4J5B | ||||
| Method | X-ray diffraction | Resolution | 2.01 Å | Mutation | Yes | [1] |
| PDB Sequence |
GNPLVYLDVD
53 ANGKPLGRVV63 LELKADVVPK73 TAENFRALCT83 GEKGFGYKGS93 TFHRVIPSFM 103 CQAGDFTNHN113 GTGGKSIYGS123 RFPDENFTLK133 HVGPGVLSMA143 NAGPNTNGSQ 153 FFICTIKTDW163 LDGKHVVFGH173 VIEGMDVVKK183 IESFGSKSGR193 TSKKIVITDC 203 GQLS
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .6B4 or .6B42 or .6B43 or :36B4;style chemicals stick;color identity;select .A:97 or .A:99 or .A:102 or .A:103 or .A:105 or .A:114 or .A:115 or .A:116 or .A:143 or .A:144 or .A:145 or .A:149 or .A:150 or .A:151 or .A:153 or .A:155 or .A:164 or .A:168; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: CypD-IN-3 | Ligand Info | |||||
| Structure Description | Structure of Cyclophilin D Peptidyl-Prolyl Isomerase Domain bound to Macrocyclic Inhibitor B52 | PDB:7THD | ||||
| Method | X-ray diffraction | Resolution | 1.16 Å | Mutation | Yes | [7] |
| PDB Sequence |
NPLVYLDVDA
54 NGKPLGRVVL64 ELKADVVPKT74 AENFRALCTG84 EKGFGYKGST94 FHRVIPSFMC 104 QAGDFTNHNG114 TGGKSIYGSR124 FPDENFTLKH134 VGPGVLSMAN144 AGPNTNGSQF 154 FICTIKTDWL164 DGKHVVFGHV174 IEGMDVVKKI184 ESFGSKSGRT194 SKKIVITDCG 204 QLS
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .I4V or .I4V2 or .I4V3 or :3I4V;style chemicals stick;color identity;select .A:96 or .A:97 or .A:99 or .A:102 or .A:103 or .A:105 or .A:113 or .A:114 or .A:115 or .A:116 or .A:117 or .A:118 or .A:119 or .A:122 or .A:123 or .A:124 or .A:125 or .A:142 or .A:143 or .A:144 or .A:145 or .A:149 or .A:150 or .A:151 or .A:152 or .A:153 or .A:154 or .A:155 or .A:163 or .A:164 or .A:168; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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HIS96
4.898
ARG97
1.957
ILE99
4.430
PHE102
2.794
MET103
3.469
GLN105
2.370
ASN113
2.780
GLY114
2.007
THR115
2.634
GLY116
2.700
GLY117
2.952
LYS118
1.798
SER119
2.159
GLY122
3.712
SER123
2.586
ARG124
2.115
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| Ligand Name: 3-[4-[4-[[(1S,4S,17S)-17-[2-(2-aminoethoxy)ethylcarbamoyl]-1-benzyl-2,5,15,21,24-pentaoxo-3,6,16,20,25-pentazatricyclo[23.3.1.08,13]nonacosa-8,10,12-trien-4-yl]methyl]phenyl]phenyl]propanoic acid | Ligand Info | |||||
| Structure Description | Structure of Cyclophilin D Peptidyl-Prolyl Isomerase Domain bound to Macrocyclic Inhibitor B23 | PDB:7TH7 | ||||
| Method | X-ray diffraction | Resolution | 1.30 Å | Mutation | Yes | [7] |
| PDB Sequence |
NPLVYLDVDA
54 NGKPLGRVVL64 ELKADVVPKT74 AENFRALCTG84 EKGFGYKGST94 FHRVIPSFMC 104 QAGDFTNHNG114 TGGKSIYGSR124 FPDENFTLKH134 VGPGVLSMAN144 AGPNTNGSQF 154 FICTIKTDWL164 DGKHVVFGHV174 IEGMDVVKKI184 ESFGSKSGRT194 SKKIVITDCG 204 QLS
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .I5E or .I5E2 or .I5E3 or :3I5E;style chemicals stick;color identity;select .A:97 or .A:99 or .A:102 or .A:103 or .A:105 or .A:113 or .A:114 or .A:115 or .A:116 or .A:117 or .A:118 or .A:119 or .A:121 or .A:122 or .A:123 or .A:124 or .A:125 or .A:142 or .A:143 or .A:144 or .A:145 or .A:149 or .A:150 or .A:151 or .A:152 or .A:153 or .A:154 or .A:155 or .A:163 or .A:164 or .A:168; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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ARG97
1.967
ILE99
4.487
PHE102
2.917
MET103
3.513
GLN105
2.391
ASN113
2.896
GLY114
2.135
THR115
2.756
GLY116
2.960
GLY117
3.256
LYS118
1.954
SER119
1.979
TYR121
4.644
GLY122
3.949
SER123
2.635
ARG124
2.455
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| Ligand Name: 3-(4'-(((13S,4S,12S,E)-12-((2-(2-aminoethoxy)ethyl)carbamoyl)-13-benzyl-2,5,10,16,19-pentaoxo-3,6,11,15-tetraaza-1(3,1)-piperidina-8(1,2)-benzenacyclononadecaphan-17-en-4-yl)methyl)-[1,1'-biphenyl]-4-yl)propiolic acid | Ligand Info | |||||
| Structure Description | Structure of Cyclophilin D Peptidyl-Prolyl Isomerase Domain bound to Macrocyclic Inhibitor B25 | PDB:7THC | ||||
| Method | X-ray diffraction | Resolution | 1.57 Å | Mutation | Yes | [7] |
| PDB Sequence |
NPLVYLDVDA
54 NGKPLGRVVL64 ELKADVVPKT74 AENFRALCTG84 EKGFGYKGST94 FHRVIPSFMC 104 QAGDFTNHNG114 TGGKSIYGSR124 FPDENFTLKH134 VGPGVLSMAN144 AGPNTNGSQF 154 FICTIKTDWL164 DGKHVVFGHV174 IEGMDVVKKI184 ESFGSKSGRT194 SKKIVITDCG 204 QLS
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .I4Z or .I4Z2 or .I4Z3 or :3I4Z;style chemicals stick;color identity;select .A:96 or .A:97 or .A:99 or .A:102 or .A:103 or .A:105 or .A:113 or .A:114 or .A:115 or .A:116 or .A:117 or .A:118 or .A:119 or .A:121 or .A:122 or .A:123 or .A:124 or .A:125 or .A:142 or .A:143 or .A:144 or .A:145 or .A:149 or .A:150 or .A:151 or .A:152 or .A:153 or .A:154 or .A:155 or .A:163 or .A:164 or .A:168; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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HIS96
4.904
ARG97
2.011
ILE99
4.336
PHE102
2.849
MET103
3.628
GLN105
2.436
ASN113
2.773
GLY114
1.989
THR115
2.514
GLY116
2.809
GLY117
3.032
LYS118
2.965
SER119
2.155
TYR121
4.898
GLY122
4.243
SER123
3.001
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Fragment-based discovery of a new family of non-peptidic small-molecule cyclophilin inhibitors with potent antiviral activities. Nat Commun. 2016 Sep 22;7:12777. | ||||
| REF 2 | Combining 'dry' co-crystallization and in situ diffraction to facilitate ligand screening by X-ray crystallography. Acta Crystallogr D Biol Crystallogr. 2015 Aug;71(Pt 8):1777-87. | ||||
| REF 3 | Human Cyclophilin D in complex with N-[(4-aminophenyl)methyl]-7-methyl-2-oxo-1H,2H-pyrazolo[1,5-a]pyrimidine-6-carboxamide | ||||
| REF 4 | Human Cyclophilin D in complex with N-(5-ethyl-4-oxo-1,2,3,4,5,6-hexahydro-1,5-benzodiazocin-8-yl)-7methyl-2-oxo-1H,2H-pyrazolo[1,5-a]pyrimidine-6-carboxamide | ||||
| REF 5 | Human Cyclophilin D Complexed with Inhibitor. | ||||
| REF 6 | Human Cyclophilin D Complexed with Inhibitor | ||||
| REF 7 | Discovery and molecular basis of subtype-selective cyclophilin inhibitors. Nat Chem Biol. 2022 Nov;18(11):1184-1195. | ||||
| REF 8 | Human Cyclophilin D Complexed with Inhibitor | ||||
| REF 9 | Human Cyclophilin D Complexed with Inhibitor. | ||||
| REF 10 | Human Cyclophilin D Complexed with Inhibitor | ||||
| REF 11 | Human Cyclophilin D Complexed with Inhibitor | ||||
| REF 12 | Discovery of novel Cyclophilin D inhibitors starting from three dimensional fragments with millimolar potencies. Bioorg Med Chem Lett. 2019 Dec 1;29(23):126717. | ||||
| REF 13 | Rationnal Design of small-molecule inhibitors of human Cyclophilins and HCV replication. | ||||
| REF 14 | Human Cyclophilin D Complexed with Inhibitor | ||||
| REF 15 | Human Cyclophilin D Complexed with Inhibitor | ||||
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