Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T34337 | Target Info | |||
| Target Name | Bacterial Undecaprenyl pyrophosphate synthetase (Bact ispU) | ||||
| Synonyms | ispU; Undecaprenyl diphosphate synthase; Undecaprenyl diphosphate synthase; UPP synthetase; UPP synthase; UDS; Di-trans-poly-cis-decaprenylcistransferase | ||||
| Target Type | Literature-reported Target | ||||
| Gene Name | Bact ispU | ||||
| Biochemical Class | Alkyl aryl transferase | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: Clomifene | Ligand Info | |||||
| Structure Description | Crystal structure of E. coli undecaprenyl pyrophosphate synthase in complex with clomiphene | PDB:5CQJ | ||||
| Method | X-ray diffraction | Resolution | 2.15 Å | Mutation | No | [1] |
| PDB Sequence |
LPAHGCRHVA
22 IIMDGNGRWA32 KKQGKIRAFG42 HKAGAKSVRR52 AVSFAANNGI62 EALTLYAFEL 88 FVWALDSEVK98 SLHRHNVRLR108 IIGDTSRFNS118 RLQERIRKSE128 ALTAGNTGLT 138 LNIAANYGGR148 WDIVQGVRQL158 AEKVQQGNLQ168 PDQIDEEMLN178 QHVCMHELAP 188 VDLVIRTGGE198 HRISNFLLWQ208 IAYAELYFTD218 VLWPDFDEQD228 FEGALNAFAN 238 RE
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| Ligand Name: Isopentenyl pyrophosphate | Ligand Info | |||||
| Structure Description | Crystal structure of the D26A mutant UPPs in complex with magnesium and isopentenyl pyrophosphate | PDB:1X09 | ||||
| Method | X-ray diffraction | Resolution | 1.87 Å | Mutation | Yes | [2] |
| PDB Sequence |
LSEKLPAHGC
18 RHVAIIMAGN28 GRWAKKQGKI38 RAFGHKAGAK48 SVRRAVSFAA58 NNGIEALTLY 68 AFSSENWNRP78 AQEVSALMEL88 FVWALDSEVK98 SLHRHNVRLR108 IIGDTSRFNS 118 RLQERIRKSE128 ALTAGNTGLT138 LNIAANYGGR148 WDIVQGVRQL158 AEKVQQGNLQ 168 PDQIDEEMLN178 QHVCMHELAP188 VDLVIRTGGE198 HRISNFLLWQ208 IAYAELYFTD 218 VLWPDFDEQD228 FEGALNAFAN238 R
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: BPH-629 | Ligand Info | |||||
| Structure Description | E. coli undecaprenyl pyrophosphate synthase in complex with BPH-629 | PDB:2E98 | ||||
| Method | X-ray diffraction | Resolution | 1.90 Å | Mutation | No | [3] |
| PDB Sequence |
AHGCRHVAII
24 MDGNGRWAKK34 QGKIRAFGHK44 AGAKSVRRAV54 SFAANNGIEA64 LTLYAFSSEN 74 WNRPAQEVSA84 LMELFVWALD94 SEVKSLHRHN104 VRLRIIGDTS114 RFNSRLQERI 124 RKSEALTAGN134 TGLTLNIAAN144 YGGRWDIVQG154 VRQLAEKVQQ164 GNLQPDQIDE 174 EMLNQHVCMH184 ELAPVDLVIR194 TGGEHRISNF204 LLWQIAYAEL214 YFTDVLWPDF 224 DEQDFEGALN234 AFANRE
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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 .B29 or .B292 or .B293 or :3B29;style chemicals stick;color identity;select .A:25 or .A:26 or .A:27 or .A:28 or .A:29 or .A:30 or .A:39 or .A:40 or .A:43 or .A:46 or .A:47 or .A:50 or .A:51 or .A:52 or .A:54 or .A:55 or .A:58 or .A:67 or .A:68 or .A:69 or .A:70 or .A:71 or .A:72 or .A:73 or .A:74 or .A:77 or .A:81 or .A:82 or .A:85 or .A:86 or .A:88 or .A:89 or .A:92 or .A:93 or .A:96 or .A:99 or .A:100 or .A:103 or .A:105 or .A:139 or .A:141 or .A:142 or .A:143 or .A:144 or .A:145 or .A:146 or .A:221; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
MET25
3.392
ASP26
3.364
GLY27
3.176
ASN28
2.741
GLY29
2.890
ARG30
4.569
ARG39
2.808
ALA40
4.285
HIS43
2.552
GLY46
4.096
ALA47
3.626
VAL50
3.769
ARG51
2.846
ARG52
4.671
VAL54
3.271
SER55
3.171
ALA58
4.795
LEU67
4.769
TYR68
2.690
ALA69
3.324
PHE70
2.600
SER71
2.604
SER72
2.996
GLU73
2.940
ASN74
3.514
ARG77
2.675
GLU81
2.387
VAL82
3.672
LEU85
3.368
MET86
3.439
LEU88
4.038
PHE89
3.397
ALA92
3.631
LEU93
3.397
GLU96
2.913
SER99
2.145
LEU100
3.478
HIS103
2.499
VAL105
4.190
LEU139
4.435
ILE141
3.449
ALA142
4.163
ALA143
3.349
ASN144
2.504
TYR145
2.648
GLY146
4.843
TRP221
4.502
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| Ligand Name: BPH-608 | Ligand Info | |||||
| Structure Description | E. coli undecaprenyl pyrophosphate synthase in complex with BPH-608 | PDB:2E99 | ||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [3] |
| PDB Sequence |
PAHGCRHVAI
23 IMDGNGRWAK33 KQGKIRAFGH43 KAGAKSVRRA53 VSFAANNGIE63 ALTLYAFSSE 73 NWNRPAQEVS83 ALMELFVWAL93 DSEVKSLHRH103 NVRLRIIGDT113 SRFNSRLQER 123 IRKSEALTAG133 NTGLTLNIAA143 NYGGRWDIVQ153 GVRQLAEKVQ163 QGNLQPDQID 173 EEMLNQHVCM183 HELAPVDLVI193 RTGGEHRISN203 FLLWQIAYAE213 LYFTDVLWPD 223 FDEQDFEGAL233 NAFANRE
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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 .B08 or .B082 or .B083 or :3B08;style chemicals stick;color identity;select .A:25 or .A:26 or .A:27 or .A:28 or .A:29 or .A:30 or .A:39 or .A:40 or .A:43 or .A:46 or .A:47 or .A:50 or .A:51 or .A:54 or .A:55 or .A:58 or .A:59 or .A:67 or .A:68 or .A:69 or .A:70 or .A:71 or .A:72 or .A:73 or .A:74 or .A:77 or .A:81 or .A:85 or .A:88 or .A:89 or .A:93 or .A:96 or .A:99 or .A:100 or .A:103 or .A:105 or .A:139 or .A:141 or .A:221; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
MET25
3.250
ASP26
3.406
GLY27
3.187
ASN28
2.922
GLY29
2.918
ARG30
4.590
ARG39
2.720
ALA40
4.537
HIS43
2.624
GLY46
4.414
ALA47
3.868
VAL50
3.576
ARG51
3.482
VAL54
3.694
SER55
3.269
ALA58
3.888
ASN59
2.954
LEU67
4.728
TYR68
4.957
ALA69
3.409
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| Ligand Name: BPH-675 | Ligand Info | |||||
| Structure Description | E. coli undecaprenyl pyrophosphate synthase in complex with BPH-675 | PDB:2E9C | ||||
| Method | X-ray diffraction | Resolution | 2.05 Å | Mutation | No | [3] |
| PDB Sequence |
PAHGCRHVAI
23 IMDGNGRWAK33 KQGKIRAFGH43 KAGAKSVRRA53 VSFAANNGIE63 ALTLYAFSSE 73 LDSEVKSLHR102 HNVRLRIIGD112 TSRFNSRLQE122 RIRKSEALTA132 GNTGLTLNIA 142 ANYGGRWDIV152 QGVRQLAEKV162 QQGNLQPDQI172 DEEMLNQHVC182 MHELAPVDLV 192 IRTGGEHRIS202 NFLLWQIAYA212 ELYFTDVLWP222 DFDEQDFEGA232 LNAFANRE |
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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 .B75 or .B752 or .B753 or :3B75;style chemicals stick;color identity;select .A:25 or .A:26 or .A:27 or .A:28 or .A:29 or .A:30 or .A:38 or .A:39 or .A:40 or .A:43 or .A:46 or .A:47 or .A:50 or .A:51 or .A:54 or .A:55 or .A:58 or .A:59 or .A:69 or .A:70 or .A:71 or .A:72 or .A:73 or .A:93 or .A:96 or .A:99 or .A:100 or .A:103 or .A:105 or .A:107 or .A:139 or .A:141 or .A:142 or .A:143 or .A:144 or .A:221; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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MET25
3.085
ASP26
3.383
GLY27
3.190
ASN28
2.740
GLY29
2.757
ARG30
4.496
ILE38
4.957
ARG39
2.650
ALA40
2.778
HIS43
2.775
GLY46
4.613
ALA47
4.323
VAL50
3.584
ARG51
2.794
VAL54
3.831
SER55
2.820
ALA58
3.717
ASN59
2.825
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| Ligand Name: BPH-628 | Ligand Info | |||||
| Structure Description | E. coli undecaprenyl pyrophosphate synthase in complex with BPH-628 | PDB:2E9A | ||||
| Method | X-ray diffraction | Resolution | 2.10 Å | Mutation | No | [3] |
| PDB Sequence |
PAHGCRHVAI
23 IMDGNGRWAK33 KQGKIRAFGH43 KAGAKSVRRA53 VSFAANNGIE63 ALTLYAFSSV 82 SALMELFVWA92 LDSEVKSLHR102 HNVRLRIIGD112 TSRFNSRLQE122 RIRKSEALTA 132 GNTGLTLNIA142 ANYGGRWDIV152 QGVRQLAEKV162 QQGNLQPDQI172 DEEMLNQHVC 182 MHELAPVDLV192 IRTGGEHRIS202 NFLLWQIAYA212 ELYFTDVLWP222 DFDEQDFEGA 232 LNAFANRE
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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 .B28 or .B282 or .B283 or :3B28;style chemicals stick;color identity;select .A:25 or .A:26 or .A:27 or .A:28 or .A:29 or .A:30 or .A:39 or .A:40 or .A:43 or .A:46 or .A:47 or .A:50 or .A:51 or .A:69 or .A:70 or .A:71 or .A:72 or .A:85 or .A:86 or .A:88 or .A:89 or .A:92 or .A:93 or .A:96 or .A:221; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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MET25
3.220
ASP26
3.680
GLY27
3.289
ASN28
2.985
GLY29
2.530
ARG30
4.443
ARG39
2.783
ALA40
3.150
HIS43
2.606
GLY46
4.556
ALA47
3.349
VAL50
4.003
ARG51
4.612
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| Ligand Name: SQ-32709 | Ligand Info | |||||
| Structure Description | Crystal structure of Undecaprenyl Pyrophosphate Synthase with farnesyl pyrophosphate | PDB:1V7U | ||||
| Method | X-ray diffraction | Resolution | 2.35 Å | Mutation | No | [4] |
| PDB Sequence |
LPAHGCRHVA
22 IIMDGNGRWA32 KKQGKIRAFG42 HKAGAKSVRR52 AVSFAANNGI62 EALTLYAFSS 72 ENWNRPAQEV82 SALMELFVWA92 LDSEVKSLHR102 HNVRLRIIGD112 TSRFNSRLQE 122 RIRKSEALTA132 GNTGLTLNIA142 ANYGGRWDIV152 QGVRQLAEKV162 QQGNLQPDQI 172 DEEMLNQHVC182 MHELAPVDLV192 IRTGGEHRIS202 NFLLWQIAYA212 ELYFTDVLWP 222 DFDEQDFEGA232 LNAFANR
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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 .FPP or .FPP2 or .FPP3 or :3FPP;style chemicals stick;color identity;select .A:25 or .A:26 or .A:27 or .A:28 or .A:29 or .A:30 or .A:31 or .A:39 or .A:43 or .A:46 or .A:47 or .A:50 or .A:51 or .A:54 or .A:55 or .A:69 or .A:81 or .A:85 or .A:88 or .A:89 or .A:91 or .A:92 or .A:93 or .A:96 or .A:97 or .A:99 or .A:100 or .A:103 or .A:107 or .A:109 or .A:139 or .A:141 or .A:221; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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MET25
3.770
ASP26
2.895
GLY27
3.354
ASN28
2.873
GLY29
3.115
ARG30
2.677
TRP31
4.863
ARG39
3.073
HIS43
3.060
GLY46
3.842
ALA47
3.722
VAL50
3.232
ARG51
3.371
VAL54
3.715
SER55
3.635
ALA69
3.240
GLU81
3.404
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| Ligand Name: BPH-676 | Ligand Info | |||||
| Structure Description | E. coli undecaprenyl pyrophosphate synthase in complex with BPH-676 | PDB:2E9D | ||||
| Method | X-ray diffraction | Resolution | 2.50 Å | Mutation | No | [3] |
| PDB Sequence |
HGCRHVAIIM
25 DGNGRWAKKQ35 GKIRAFGHKA45 GAKSVRRAVS55 FAANNGIEAL65 TLYAFSAQEV 82 SALMELFVWA92 LDSEVKSLHR102 HNVRLRIIGD112 TSRFNSRLQE122 RIRKSEALTA 132 GNTGLTLNIA142 ANYGGRWDIV152 QGVRQLAEKV162 QQGNLQPDQI172 DEEMLNQHVC 182 MHELAPVDLV192 IRTGGEHRIS202 NFLLWQIAYA212 ELYFTDVLWP222 DFDEQDFEGA 232 LNAFANRE
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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 .B76 or .B762 or .B763 or :3B76;style chemicals stick;color identity;select .A:25 or .A:26 or .A:27 or .A:28 or .A:29 or .A:39 or .A:43 or .A:46 or .A:47 or .A:50 or .A:51 or .A:54 or .A:55 or .A:59 or .A:67 or .A:69 or .A:70 or .A:71 or .A:85 or .A:88 or .A:93 or .A:96 or .A:99 or .A:100 or .A:103 or .A:105 or .A:139 or .A:141 or .A:221; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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MET25
4.449
ASP26
4.491
GLY27
4.919
ASN28
2.824
GLY29
3.731
ARG39
3.760
HIS43
2.593
GLY46
4.470
ALA47
4.489
VAL50
3.298
ARG51
3.846
VAL54
3.206
SER55
3.032
ASN59
3.682
LEU67
4.862
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| Ligand Name: 2-{[3-(3,4-Dimethylphenoxy)phenyl]carbamoyl}-4-Nitrobenzoic Acid | Ligand Info | |||||
| Structure Description | Crystal Structure of E. coli undecaprenyl pyrophosphate synthase in complex with BPH-1290 | PDB:3SGV | ||||
| Method | X-ray diffraction | Resolution | 1.61 Å | Mutation | No | [5] |
| PDB Sequence |
LPAHGCRHVA
22 IIMDGNGRWA32 KKQGKIRAFG42 HKAGAKSVRR52 AVSFAANNGI62 EALTLYAFVS 83 ALMELFVWAL93 DSEVKSLHRH103 NVRLRIIGDT113 SRFNSRLQER123 IRKSEALTAG 133 NTGLTLNIAA143 NYGGRWDIVQ153 GVRQLAEKVQ163 QGNLQPDQID173 EEMLNQHVCM 183 HELAPVDLVI193 RTGGEHRISN203 FLLWQIAYAE213 LYFTDVLWPD223 FDEQDFEGAL 233 NAFANRE
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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 .2BJ or .2BJ2 or .2BJ3 or :32BJ;style chemicals stick;color identity;select .B:25 or .B:26 or .B:27 or .B:28 or .B:29 or .B:30 or .B:39 or .B:40 or .B:42 or .B:43 or .B:44 or .B:46 or .B:47 or .B:48 or .B:50 or .B:51 or .B:69 or .B:70 or .B:82 or .B:85 or .B:88 or .B:89 or .B:91 or .B:92 or .B:93 or .B:96 or .B:100 or .B:139 or .B:141; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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MET25
3.223
ASP26
3.637
GLY27
3.023
ASN28
2.657
GLY29
2.980
ARG30
4.631
ARG39
3.710
ALA40
4.859
GLY42
4.749
HIS43
3.290
LYS44
3.179
GLY46
3.889
ALA47
3.418
LYS48
1.758
VAL50
3.344
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|||||
| Ligand Name: 2,2'-{benzene-1,3-Diylbis[ethyne-2,1-Diyl(5-Bromobenzene-3,1-Diyl)]}diethanamine | Ligand Info | |||||
| Structure Description | Structure of E. coli undecaprenyl diphosphate synthase in complex with BPH-1408 | PDB:4H2M | ||||
| Method | X-ray diffraction | Resolution | 1.78 Å | Mutation | No | [5] |
| PDB Sequence |
AHGCRHVAII
24 MDGNGRWAKK34 QGKIRAFGHK44 AGAKSVRRAV54 SFAANNGIEA64 LTLYAFSSLM 86 ELFVWALDSE96 VKSLHRHNVR106 LRIIGDTSRF116 NSRLQERIRK126 SEALTAGNTG 136 LTLNIAANYG146 GRWDIVQGVR156 QLAEKVQQGN166 LQPDQIDEEM176 LNQHVCMHEL 186 APVDLVIRTG196 GEHRISNFLL206 WQIAYAELYF216 TDVLWPDFDE226 QDFEGALNAF 236 ANRE
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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 .0YV or .0YV2 or .0YV3 or :30YV;style chemicals stick;color identity;select .A:43 or .A:44 or .A:47 or .A:50 or .A:51 or .A:54 or .A:55 or .A:58 or .A:89 or .A:92 or .A:93 or .A:96 or .A:99 or .A:100 or .A:103 or .A:105 or .A:139 or .A:141; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 2-(2-{2-[2-(2-{2-[2-(2-{2-[4-(1,1,3,3-Tetramethyl-butyl)-phenoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethanol | Ligand Info | |||||
| Structure Description | Structure of E.coli undecaprenyl pyrophosphate synthase | PDB:1JP3 | ||||
| Method | X-ray diffraction | Resolution | 1.80 Å | Mutation | Yes | [6] |
| PDB Sequence |
LPAHGCRHVA
22 IIDGNGRWAK33 KQGKIRAFGH43 KAGAKSVRRA53 VSFAANNGIE63 ALTLYAFSEL 88 FVWALDSEVK98 SLHRHNVRLR108 IIGDTSRFNS118 RLQERIRKSE128 ALTAGNTGLT 138 LNIAANYGGR148 WDIVQGVRQL158 AEKVQQGNLQ168 PDQIDEELNQ179 HVCHELAPVD 190 LVIRTGGEHR200 ISNFLLWQIA210 YAELYFTDVL220 WPDFDEQDFE230 GALNAFANRE 240
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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 .EGC or .EGC2 or .EGC3 or :3EGC;style chemicals stick;color identity;select .A:69 or .A:88 or .A:89 or .A:92 or .A:96 or .A:100 or .A:141 or .A:142 or .A:143 or .A:144; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: Selenomethionine | Ligand Info | |||||
| Structure Description | Structure of E.coli undecaprenyl pyrophosphate synthase | PDB:1JP3 | ||||
| Method | X-ray diffraction | Resolution | 1.80 Å | Mutation | Yes | [6] |
| PDB Sequence |
LPAHGCRHVA
22 IIDGNGRWAK33 KQGKIRAFGH43 KAGAKSVRRA53 VSFAANNGIE63 ALTLYAFSEL 88 FVWALDSEVK98 SLHRHNVRLR108 IIGDTSRFNS118 RLQERIRKSE128 ALTAGNTGLT 138 LNIAANYGGR148 WDIVQGVRQL158 AEKVQQGNLQ168 PDQIDEELNQ179 HVCHELAPVD 190 LVIRTGGEHR200 ISNFLLWQIA210 YAELYFTDVL220 WPDFDEQDFE230 GALNAFANRE 240
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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 .MSE or .MSE2 or .MSE3 or :3MSE;style chemicals stick;color identity;select .A:20 or .A:23 or .A:24 or .A:26 or .A:27 or .A:50 or .A:66 or .A:67 or .A:68 or .A:69 or .A:70 or .A:87 or .A:88 or .A:89 or .A:90 or .A:91 or .A:110 or .A:116 or .A:120 or .A:140 or .A:158 or .A:167 or .A:171 or .A:172 or .A:173 or .A:174 or .A:175 or .A:177 or .A:178 or .A:179 or .A:180 or .A:181 or .A:182 or .A:184 or .A:185 or .A:186 or .A:187 or .A:189 or .A:195 or .A:205 or .A:208 or .A:221; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
HIS20
3.837
ILE23
3.576
ILE24
1.323
ASP26
1.324
GLY27
4.541
VAL50
3.571
THR66
3.187
LEU67
3.884
TYR68
2.853
ALA69
3.631
PHE70
3.046
GLU87
1.327
LEU88
3.583
PHE89
3.398
VAL90
2.737
TRP91
4.773
ILE110
4.075
PHE116
3.435
LEU120
3.934
ASN140
3.459
LEU158
3.669
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|||||
| Ligand Name: N~4~-[4-(4,5-Dihydro-1h-Imidazol-2-Yl)phenyl]-N~1~-[4-(1h-Imidazol-2-Yl)phenyl]-2-Nitrobenzene-1,4-Dicarboxamide | Ligand Info | |||||
| Structure Description | Structure of E. coli undecaprenyl diphosphate synthase in complex with BPH-1354 | PDB:4H2J | ||||
| Method | X-ray diffraction | Resolution | 1.81 Å | Mutation | No | [5] |
| PDB Sequence |
LPAHGCRHVA
22 IIMDGNGRWA32 KKQGKIRAFG42 HKAGAKSVRR52 AVSFAANNGI62 EALTLYAFSS 72 ELMELFVWAL93 DSEVKSLHRH103 NVRLRIIGDT113 SRFNSRLQER123 IRKSEALTAG 133 NTGLTLNIAA143 NYGGRWDIVQ153 GVRQLAEKVQ163 QGNLQPDQID173 EEMLNQHVCM 183 HELAPVDLVI193 RTGGEHRISN203 FLLWQIAYAE213 LYFTDVLWPD223 FDEQDFEGAL 233 NAFANRE
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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 .0YU or .0YU2 or .0YU3 or :30YU;style chemicals stick;color identity;select .A:40 or .A:43 or .A:44 or .A:47 or .A:50 or .A:51 or .A:54 or .A:55 or .A:67 or .A:89 or .A:92 or .A:93 or .A:96 or .A:99 or .A:100 or .A:103 or .A:139 or .A:141; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 2-(Dodecyloxy)-6-Hydroxybenzoic Acid | Ligand Info | |||||
| Structure Description | Crystal Structure of E. coli undecaprenyl pyrophosphate synthase in complex with BPH-1065 | PDB:3SH0 | ||||
| Method | X-ray diffraction | Resolution | 1.84 Å | Mutation | No | [5] |
| PDB Sequence |
LPAHGCRHVA
22 IIMDGNGRWA32 KKQGKIRAFG42 HKAGAKSVRR52 AVSFAANNGI62 EALTLYAFSS 72 AQEVSALMEL88 FVWALDSEVK98 SLHRHNVRLR108 IIGDTSRFNS118 RLQERIRKSE 128 ALTAGNTGLT138 LNIAANYGGR148 WDIVQGVRQL158 AEKVQQGNLQ168 PDQIDEEMLN 178 QHVCMHELAP188 VDLVIRTGGE198 HRISNFLLWQ208 IAYAELYFTD218 VLWPDFDEQD 228 FEGALNAFAN238 RE
|
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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 .SAX or .SAX2 or .SAX3 or :3SAX;style chemicals stick;color identity;select .B:25 or .B:47 or .B:50 or .B:51 or .B:54 or .B:55 or .B:58 or .B:59 or .B:69 or .B:82 or .B:85 or .B:86 or .B:88 or .B:89 or .B:91 or .B:92 or .B:93 or .B:96 or .B:97 or .B:99 or .B:100 or .B:103 or .B:105 or .B:107 or .B:109 or .B:116 or .B:139 or .B:141 or .B:142 or .B:143 or .B:144 or .B:145; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
MET25
4.180
ALA47
3.675
VAL50
3.829
ARG51
3.763
VAL54
3.910
SER55
3.153
ALA58
3.204
ASN59
2.983
ALA69
4.029
VAL82
4.060
LEU85
3.506
MET86
3.669
LEU88
3.771
PHE89
3.894
TRP91
3.830
ALA92
3.795
|
|||||
| Ligand Name: Farnesyl thiopyrophosphate | Ligand Info | |||||
| Structure Description | Crystal structure of undecaprenyl pyrophosphate synthase in complex with Mg, IPP and Fspp | PDB:1X06 | ||||
| Method | X-ray diffraction | Resolution | 1.90 Å | Mutation | No | [2] |
| PDB Sequence |
KLPAHGCRHV
21 AIIMDGNGRW31 AKKQGKIRAF41 GHKAGAKSVR51 RAVSFAANNG61 IEALTLYAFS 71 SENWNRPAQE81 VSALMELFVW91 ALDSEVKSLH101 RHNVRLRIIG111 DTSRFNSRLQ 121 ERIRKSEALT131 AGNTGLTLNI141 AANYGGRWDI151 VQGVRQLAEK161 VQQGNLQPDQ 171 IDEEMLNQHV181 CMHELAPVDL191 VIRTGGEHRI201 SNFLLWQIAY211 AELYFTDVLW 221 PDFDEQDFEG231 ALNAFANRE
|
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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 .FPS or .FPS2 or .FPS3 or :3FPS;style chemicals stick;color identity;select .A:25 or .A:26 or .A:27 or .A:28 or .A:29 or .A:30 or .A:39 or .A:43 or .A:46 or .A:47 or .A:50 or .A:51 or .A:54 or .A:68 or .A:69 or .A:70 or .A:74 or .A:77 or .A:81 or .A:85 or .A:88 or .A:89 or .A:92 or .A:93 or .A:96 or .A:97 or .A:100 or .A:107 or .A:109 or .A:139 or .A:141 or .A:221; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
MET25
3.662
ASP26
2.824
GLY27
3.555
ASN28
3.058
GLY29
2.940
ARG30
2.778
ARG39
2.541
HIS43
2.934
GLY46
3.844
ALA47
3.813
VAL50
3.405
ARG51
3.872
VAL54
4.450
TYR68
3.994
ALA69
3.455
PHE70
4.934
|
|||||
| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: (2z)-4-[3-(Decyloxy)phenyl]-2-Hydroxy-4-Oxobut-2-Enoic Acid | Ligand Info | |||||
| Structure Description | Structure of E. coli undecaprenyl diphosphate synthase in complex with BPH-987 | PDB:4H3C | ||||
| Method | X-ray diffraction | Resolution | 1.93 Å | Mutation | No | [5] |
| PDB Sequence |
AHGCRHVAII
24 MDGNGRWAKK34 QGKIRAFGHK44 AGAKSVRRAV54 SFAANNGIEA64 LTLYAFMELF 89 VWALDSEVKS99 LHRHNVRLRI109 IGDTSRFNSR119 LQERIRKSEA129 LTAGNTGLTL 139 NIAANYGGRW149 DIVQGVRQLA159 EKVQQGNLQP169 DQIDEEMLNQ179 HVCMHELAPV 189 DLVIRTGGEH199 RISNFLLWQI209 AYAELYFTDV219 LWPDFDEQDF229 EGALNAFANR 239
|
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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 .0YZ or .0YZ2 or .0YZ3 or :30YZ;style chemicals stick;color identity;select .A:47 or .A:50 or .A:51 or .A:54 or .A:55 or .A:58 or .A:59 or .A:68 or .A:69 or .A:86 or .A:87 or .A:89 or .A:90 or .A:93 or .A:96 or .A:97 or .A:99 or .A:100 or .A:103 or .A:105 or .A:107 or .A:116 or .A:139 or .A:141 or .A:142 or .A:143 or .A:144 or .A:145; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ALA47
3.691
VAL50
4.007
ARG51
3.755
VAL54
3.679
SER55
3.069
ALA58
3.405
ASN59
3.108
TYR68
3.088
ALA69
4.101
MET86
4.261
GLU87
3.425
PHE89
4.988
VAL90
3.567
LEU93
3.538
|
|||||
| Ligand Name: (5-Bromo-2-{[3-(Octyloxy)benzyl]oxy}phenyl)phosphonic Acid | Ligand Info | |||||
| Structure Description | Structure of E. coli undecaprenyl diphosphate synthase in complex with BPH-1297 | PDB:4H38 | ||||
| Method | X-ray diffraction | Resolution | 1.95 Å | Mutation | No | [5] |
| PDB Sequence |
AHGCRHVAII
24 MDGNGRWAKK34 QGKIRAFGHK44 AGAKSVRRAV54 SFAANNGIEA64 LTLYAFSSLM 86 ELFVWALDSE96 VKSLHRHNVR106 LRIIGDTSRF116 NSRLQERIRK126 SEALTAGNTG 136 LTLNIAANYG146 GRWDIVQGVR156 QLAEKVQQGN166 LQPDQIDEEM176 LNQHVCMHEL 186 APVDLVIRTG196 GEHRISNFLL206 WQIAYAELYF216 TDVLWPDFDE226 QDFEGALNAF 236 ANRE
|
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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 .0YX or .0YX2 or .0YX3 or :30YX;style chemicals stick;color identity;select .A:40 or .A:43 or .A:44 or .A:47 or .A:50 or .A:51 or .A:54 or .A:55 or .A:89 or .A:92 or .A:93 or .A:96 or .A:99 or .A:100 or .A:103 or .A:139 or .A:141; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: (2z)-2-Hydroxy-4-[4-(Octyloxy)phenyl]-4-Oxobut-2-Enoic Acid | Ligand Info | |||||
| Structure Description | Structure of E. coli undecaprenyl diphosphate synthase in complex with BPH-1330 | PDB:4H3A | ||||
| Method | X-ray diffraction | Resolution | 1.98 Å | Mutation | No | [5] |
| PDB Sequence |
AHGCRHVAII
24 MDGNGRWAKK34 QGKIRAFGHK44 AGAKSVRRAV54 SFAANNGIEA64 LTLYAFLFVW 91 ALDSEVKSLH101 RHNVRLRIIG111 DTSRFNSRLQ121 ERIRKSEALT131 AGNTGLTLNI 141 AANYGGRWDI151 VQGVRQLAEK161 VQQGNLQPDQ171 IDEEMLNQHV181 CMHELAPVDL 191 VIRTGGEHRI201 SNFLLWQIAY211 AELYFTDVLW221 PDFDEQDFEG231 ALNAFANR |
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .0YY or .0YY2 or .0YY3 or :30YY;style chemicals stick;color identity;select .A:47 or .A:50 or .A:51 or .A:54 or .A:55 or .A:89 or .A:93 or .A:96 or .A:99 or .A:100 or .A:103 or .A:139; 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-Oxidanyl-2-[3-[3-[[3-[[3-[3-(2-oxidanyl-2,2-diphosphono-ethyl)phenyl]phenyl]sulfamoyl]phenyl]sulfonylamino]phenyl]phenyl]-1-phosphono-ethyl]phosphonic acid | Ligand Info | |||||
| Structure Description | Structure of E. coli undecaprenyl diphosphate synthase in complex with BPH-789 | PDB:3WYJ | ||||
| Method | X-ray diffraction | Resolution | 2.10 Å | Mutation | No | [7] |
| PDB Sequence |
PAHGCRHVAI
23 IMDGNGRWAK33 KQGKIRAFGH43 KAGAKSVRRA53 VSFAANNGIE63 ALTLYAFSSP 78 AQEVSALMEL88 FVWALDSEVK98 SLHRHNVRLR108 IIGDTSRFNS118 RLQERIRKSE 128 ALTAGNTGLT138 LNIAANYGGR148 WDIVQGVRQL158 AEKVQQGNLQ168 PDQIDEEMLN 178 QHVCMHELAP188 VDLVIRTGGE198 HRISNFLLWQ208 IAYAELYFTD218 VLWPDFDEQD 228 FEGALNAFAN238 RE
|
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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 .H78 or .H782 or .H783 or :3H78;style chemicals stick;color identity;select .A:25 or .A:26 or .A:27 or .A:28 or .A:29 or .A:30 or .A:39 or .A:40 or .A:43 or .A:46 or .A:47 or .A:50 or .A:68 or .A:69 or .A:70 or .A:71 or .A:72 or .A:85 or .A:86 or .A:88 or .A:89 or .A:92 or .A:141 or .A:142 or .A:143 or .A:221; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
MET25
3.150
ASP26
3.248
GLY27
3.140
ASN28
2.880
GLY29
2.662
ARG30
4.461
ARG39
2.981
ALA40
3.291
HIS43
2.725
GLY46
4.457
ALA47
3.641
VAL50
3.773
TYR68
4.993
|
|||||
| Ligand Name: (2z)-4-({3-[3-(Hexyloxy)phenyl]propyl}amino)-2-Hydroxy-4-Oxobut-2-Enoic Acid | Ligand Info | |||||
| Structure Description | Structure of E. coli undecaprenyl diphosphate synthase complexed with BPH-1063 | PDB:3TH8 | ||||
| Method | X-ray diffraction | Resolution | 2.11 Å | Mutation | No | [8] |
| PDB Sequence |
PAHGCRHVAI
23 IMDGNGRWAK33 KQGKIRAFGH43 KAGAKSVRRA53 VSFAANNGIE63 ALTLYAFMEL 88 FVWALDSEVK98 SLHRHNVRLR108 IIGDTSRFNS118 RLQERIRKSE128 ALTAGNTGLT 138 LNIAANYGGR148 WDIVQGVRQL158 AEKVQQGNLQ168 PDQIDEEMLN178 QHVCMHELAP 188 VDLVIRTGGE198 HRISNFLLWQ208 IAYAELYFTD218 VLWPDFDEQD228 FEGALNAFAN 238 R
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .TH9 or .TH92 or .TH93 or :3TH9;style chemicals stick;color identity;select .B:25 or .B:26 or .B:27 or .B:28 or .B:29 or .B:30 or .B:39 or .B:43 or .B:46 or .B:47 or .B:50 or .B:69 or .B:70 or .B:92 or .B:93 or .B:96 or .B:100 or .B:139 or .B:141 or .B:221; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 2-{[3-(Decyloxy)benzoyl]amino}-5-Nitrobenzoic Acid | Ligand Info | |||||
| Structure Description | Structure of E. coli undecaprenyl diphosphate synthase in complex with BPH-1248 | PDB:4H2O | ||||
| Method | X-ray diffraction | Resolution | 2.14 Å | Mutation | No | [5] |
| PDB Sequence |
PAHGCRHVAI
23 IMDGNGRWAK33 KQGKIRAFGH43 KAGAKSVRRA53 VSFAANNGIE63 ALTLYAFSSF 89 VWALDSEVKS99 LHRHNVRLRI109 IGDTSRFNSR119 LQERIRKSEA129 LTAGNTGLTL 139 NIAANYGGRW149 DIVQGVRQLA159 EKVQQGQPDQ171 IDEEMLNQHV181 CMHELAPVDL 191 VIRTGGEHRI201 SNFLLWQIAY211 AELYFTDVLW221 PDFDEQDFEG231 ALNAFANR |
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .0YW or .0YW2 or .0YW3 or :30YW;style chemicals stick;color identity;select .B:47 or .B:50 or .B:51 or .B:54 or .B:55 or .B:58 or .B:59 or .B:69 or .B:89 or .B:90 or .B:93 or .B:96 or .B:97 or .B:99 or .B:100 or .B:103 or .B:105 or .B:107 or .B:109 or .B:116 or .B:139 or .B:141 or .B:142 or .B:143 or .B:144 or .B:145; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ALA47
3.526
VAL50
3.753
ARG51
3.309
VAL54
3.683
SER55
2.861
ALA58
4.371
ASN59
4.231
ALA69
3.935
PHE89
2.331
VAL90
3.719
LEU93
3.357
GLU96
3.329
VAL97
4.483
|
|||||
| Ligand Name: 4-{3-[(Biphenyl-4-ylcarbonyl)amino]phenoxy}benzene-1,2-dicarboxylic acid | Ligand Info | |||||
| Structure Description | Crystal Structure of E. coli undecaprenyl pyrophosphate synthase in complex with BPH-1100 | PDB:3SGX | ||||
| Method | X-ray diffraction | Resolution | 2.45 Å | Mutation | No | [5] |
| PDB Sequence |
GCRHVAIIMD
26 GNGRWAKKQG36 KIRAFGHKAG46 AKSVRRAVSF56 AANNGIEALT66 LYAFSSELME 87 LFVWALDSEV97 KSLHRHNVRL107 RIIGDTSRFN117 SRLQERIRKS127 EALTAGNTGL 137 TLNIAANYGG147 RWDIVQGVRQ157 LAEKVQQGNL167 QPDQIDEEML177 NQHVCMHELA 187 PVDLVIRTGG197 EHRISNFLLW207 QIAYAELYFT217 DVLWPDFDEQ227 DFEGALNAFA 237 N
|
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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 .0FW or .0FW2 or .0FW3 or :30FW;style chemicals stick;color identity;select .A:25 or .A:28 or .A:29 or .A:39 or .A:42 or .A:43 or .A:46 or .A:47 or .A:50 or .A:51 or .A:54 or .A:55 or .A:58 or .A:59 or .A:67 or .A:69 or .A:70 or .A:71 or .A:72 or .A:73 or .A:85 or .A:86 or .A:88 or .A:89 or .A:91 or .A:92 or .A:93 or .A:95 or .A:96 or .A:99 or .A:100 or .A:103 or .A:105 or .A:107 or .A:109 or .A:139 or .A:141; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
MET25
3.867
ASN28
3.095
GLY29
3.975
ARG39
2.851
GLY42
4.849
HIS43
2.973
GLY46
4.590
ALA47
3.454
VAL50
3.658
ARG51
3.731
VAL54
3.362
SER55
3.457
ALA58
3.373
ASN59
3.117
LEU67
4.717
ALA69
3.595
PHE70
3.356
SER71
3.300
SER72
4.780
|
|||||
| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Antagonism screen for inhibitors of bacterial cell wall biogenesis uncovers an inhibitor of undecaprenyl diphosphate synthase. Proc Natl Acad Sci U S A. 2015 Sep 1;112(35):11048-53. | ||||
| REF 2 | Crystal structures of undecaprenyl pyrophosphate synthase in complex with magnesium, isopentenyl pyrophosphate, and farnesyl thiopyrophosphate: roles of the metal ion and conserved residues in catalysis. J Biol Chem. 2005 May 27;280(21):20762-74. | ||||
| REF 3 | Bisphosphonates target multiple sites in both cis- and trans-prenyltransferases. Proc Natl Acad Sci U S A. 2007 Jun 12;104(24):10022-7. | ||||
| REF 4 | Substrate binding mode and reaction mechanism of undecaprenyl pyrophosphate synthase deduced from crystallographic studies. Protein Sci. 2004 Apr;13(4):971-8. | ||||
| REF 5 | Antibacterial drug leads targeting isoprenoid biosynthesis. Proc Natl Acad Sci U S A. 2013 Jan 2;110(1):123-8. | ||||
| REF 6 | Mechanism of product chain length determination and the role of a flexible loop in Escherichia coli undecaprenyl-pyrophosphate synthase catalysis. J Biol Chem. 2001 Dec 14;276(50):47474-82. | ||||
| REF 7 | Antibacterial drug leads: DNA and enzyme multitargeting. J Med Chem. 2015 Feb 12;58(3):1215-27. | ||||
| REF 8 | HIV-1 Integrase Inhibitor-Inspired Antibacterials Targeting Isoprenoid Biosynthesis. ACS Med Chem Lett. 2012 Apr 3;3(5):402-406. | ||||
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