Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T70521 | Target Info | |||
| Target Name | Bacterial MTA/SAH nucleosidase (Bact mtnN) | ||||
| Synonyms | mtnN; S-adenosylhomocysteine nucleosidase; P46; 5'-methylthioadenosine nucleosidase; 5'-Methylthioadenosine/S-adenosylhomocysteine (MTA/AdoHcy) nucleosidase | ||||
| Target Type | Literature-reported Target | ||||
| Gene Name | Bact mtnN | ||||
| Biochemical Class | Glycosylase | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: Adenine | Ligand Info | |||||
| Structure Description | Crystal Structure of E. coli MTA/AdoHcy Nucleosidase | PDB:1JYS | ||||
| Method | X-ray diffraction | Resolution | 1.90 Å | Mutation | No | [1] |
| PDB Sequence |
MKIGIIGAME
10 EEVTLLRDKI20 ENRQTISLGG30 CEIYTGQLNG40 TEVALLKSGI50 GKVAAALGAT 60 LLLEHCKPDV70 IINTGSAGGL80 APTLKVGDIV90 VSDEARYHDA100 DVTAFGYEYG 110 QLPGCPAGFK120 ADDKLIAAAE130 ACIAELNLNA140 VRGLIVSGDA150 FINGSVGLAK 160 IRHNFPQAIA170 VEMEATAIAH180 VCHNFNVPFV190 VVRAISDVAD200 QSFDEFLAVA 214 AKQSSLMVES224 LVQKLA
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 5'-Deoxy-5'-(Methylthio)-Tubercidin | Ligand Info | |||||
| Structure Description | Crystal structure of E. coli MTA/AdoHcy nucleosidase complexed with 5'-methylthiotubercidin (MTH) | PDB:1NC1 | ||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [2] |
| PDB Sequence |
FSMKIGIIGA
8 MEEEVTLLRD18 KIENRQTISL28 GGCEIYTGQL38 NGTEVALLKS48 GIGKVAAALG 58 ATLLLEHCKP68 DVIINTGSAG78 GLAPTLKVGD88 IVVSDEARYH98 DADVTAFGYE 108 YGQLPGCPAG118 FKADDKLIAA128 AEACIAELNL138 NAVRGLIVSG148 DAFINGSVGL 158 AKIRHNFPQA168 IAVEMEATAI178 AHVCHNFNVP188 FVVVRAISDV198 ADQQSHLSFD 208 EFLAVAAKQS218 SLMVESLVQK228 LAHG
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| Ligand Name: Methylthioadenosine | Ligand Info | |||||
| Structure Description | Crystal structure of MTA/AdoHcy nucleosidase Asp197Asn mutant complexed with 5'-methylthioadenosine | PDB:1Z5O | ||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | Yes | [3] |
| PDB Sequence |
EFSMKIGIIG
7 AMEEEVTLLR17 DKIENRQTIS27 LGGCEIYTGQ37 LNGTEVALLK47 SGIGKVAAAL 57 GATLLLEHCK67 PDVIINTGSA77 GGLAPTLKVG87 DIVVSDEARY97 HDADVTAFGY 107 EYGQLPGCPA117 GFKADDKLIA127 AAEACIAELN137 LNAVRGLIVS147 GDAFINGSVG 157 LAKIRHNFPQ167 AIAVEMEATA177 IAHVCHNFNV187 PFVVVRAISN197 VADQQSHLSF 207 DEFLAVAAKQ217 SSLMVESLVQ227 KLAHG
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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 .MTA or .MTA2 or .MTA3 or :3MTA;style chemicals stick;color identity;select .A:8 or .A:9 or .A:12 or .A:50 or .A:76 or .A:77 or .A:78 or .A:150 or .A:151 or .A:152 or .A:171 or .A:172 or .A:173 or .A:174 or .A:193 or .A:196 or .A:197 or .A:199 or .A:203 or .A:207; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: Formycin | Ligand Info | |||||
| Structure Description | Crystal structure of E. coli MTA/AdoHcy nucleosidase complexed with formycin A (FMA) | PDB:1NC3 | ||||
| Method | X-ray diffraction | Resolution | 2.20 Å | Mutation | No | [2] |
| PDB Sequence |
EFSMKIGIIG
7 AMEEEVTLLR17 DKIENRQTIS27 LGGCEIYTGQ37 LNGTEVALLK47 SGIGKVAAAL 57 GATLLLEHCK67 PDVIINTGSA77 GGLAPTLKVG87 DIVVSDEARY97 HDADVTAFGY 107 EYGQLPGCPA117 GFKADDKLIA127 AAEACIAELN137 LNAVRGLIVS147 GDAFINGSVG 157 LAKIRHNFPQ167 AIAVEMEATA177 IAHVCHNFNV187 PFVVVRAISD197 VADQQSHLSF 207 DEFLAVAAKQ217 SSLMVESLVQ227 KLAHG
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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 .FMC or .FMC2 or .FMC3 or :3FMC;style chemicals stick;color identity;select .A:8 or .A:9 or .A:50 or .A:76 or .A:77 or .A:78 or .A:150 or .A:151 or .A:152 or .A:171 or .A:172 or .A:173 or .A:174 or .A:193 or .A:196 or .A:197 or .A:199 or .A:203 or .A:207; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: (3r,4s)-1-[(4-Amino-5h-Pyrrolo[3,2-D]pyrimidin-7-Yl)methyl]-4-{[(4-Chlorophenyl)sulfanyl]methyl}pyrrolidin-3-Ol | Ligand Info | |||||
| Structure Description | Crystal structure of E. coli MTA/SAH nucleosidase in complex with (4-Chlorophenyl)thio-DADMe-ImmA | PDB:3O4V | ||||
| Method | X-ray diffraction | Resolution | 1.75 Å | Mutation | No | [4] |
| PDB Sequence |
FSMKIGIIGA
8 MEEEVTLLRD18 KIENRQTISL28 GGCEIYTGQL38 NGTEVALLKS48 GIGKVAAALG 58 ATLLLEHCKP68 DVIINTGSAG78 GLAPTLKVGD88 IVVSDEARYH98 DADVTAFGYE 108 YGQLPGCPAG118 FKADDKLIAA128 AEACIAELNL138 NAVRGLIVSG148 DAFINGSVGL 158 AKIRHNFPQA168 IAVEMEATAI178 AHVCHNFNVP188 FVVVRAISDV198 ADQQSHLSFD 208 EFLAVAAKQS218 SLMVESLVQK228 LAHG
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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 .4CT or .4CT2 or .4CT3 or :34CT;style chemicals stick;color identity;select .A:8 or .A:9 or .A:12 or .A:50 or .A:51 or .A:76 or .A:77 or .A:78 or .A:150 or .A:151 or .A:152 or .A:171 or .A:172 or .A:173 or .A:174 or .A:193 or .A:196 or .A:197 or .A:199 or .A:203 or .A:207; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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ALA8
3.755
MET9
3.872
GLU12
3.821
ILE50
3.488
GLY51
4.913
SER76
3.252
ALA77
3.491
GLY78
3.352
ALA150
3.511
PHE151
3.387
ILE152
2.960
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| Ligand Name: 3,6,9,12,15,18,21,24-Octaoxahexacosan-1-OL | Ligand Info | |||||
| Structure Description | Crystal structure of MTA/AdoHcy nucleosidase with a ligand-free purine binding site | PDB:1Z5P | ||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [3] |
| PDB Sequence |
MKIGIIGAME
10 EEVTLLRDKI20 ENRQTISLGG30 CEIYTGQLNG40 TEVALLKSGI50 GKVAAALGAT 60 LLLEHCKPDV70 IINTGSAGGL80 APTLKVGDIV90 VSDEARYHDA100 DVTAFGYEYG 110 QLPGCPAGFK120 ADDKLIAAAE130 ACIAELNLNA140 VRGLIVSGDA150 FINGSVGLAK 160 IRHNFPQAIA170 VEMEATAIAH180 VCHNFNVPFV190 VVRAISDVAD200 QQSHLSFDEF 210 LAVAAKQSSL220 MVESLVQKLA230 HG
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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 .PE5 or .PE52 or .PE53 or :3PE5;style chemicals stick;color identity;select .A:39 or .A:50 or .A:135 or .A:136 or .A:151 or .A:173 or .A:207 or .A:220 or .A:223 or .A:224 or .A:227; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 5-S-Methyl-5-thio-alpha-D-ribofuranose | Ligand Info | |||||
| Structure Description | Crystal structure of MTA/AdoHcy nucleosidase Glu12Gln mutant complexed with 5-methylthioribose and adenine | PDB:1Z5N | ||||
| Method | X-ray diffraction | Resolution | 2.10 Å | Mutation | Yes | [3] |
| PDB Sequence |
FSMKIGIIGA
8 MEEQVTLLRD18 KIENRQTISL28 GGCEIYTGQL38 NGTEVALLKS48 GIGKVAAALG 58 ATLLLEHCKP68 DVIINTGSAG78 GLAPTLKVGD88 IVVSDEARYH98 DADVTAFGYE 108 YGQLPGCPAG118 FKADDKLIAA128 AEACIAELNL138 NAVRGLIVSG148 DAFINGSVGL 158 AKIRHNFPQA168 IAVEMEATAI178 AHVCHNFNVP188 FVVVRAISDV198 ADQQSHLSFD 208 EFLAVAAKQS218 SLMVESLVQK228 LAHG
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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 .SR1 or .SR12 or .SR13 or :3SR1;style chemicals stick;color identity;select .A:8 or .A:9 or .A:12 or .A:50 or .A:51 or .A:75 or .A:76 or .A:151 or .A:172 or .A:173 or .A:174 or .A:193 or .A:207; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: (2S,3S,4R,5S)-2-(4-Amino-4,5-dihydro-1H-pyrrolo[3,2-d]pyrimidin-7-yl)-5-[(methylsulfanyl)methyl]-3,4-pyrrolidinediol | Ligand Info | |||||
| Structure Description | Crystal structure of MTA/AdoHcy nucleosidase complexed with MT-ImmA. | PDB:1Y6R | ||||
| Method | X-ray diffraction | Resolution | 2.20 Å | Mutation | No | [5] |
| PDB Sequence |
FSMKIGIIGA
8 MEEEVTLLRD18 KIENRQTISL28 GGCEIYTGQL38 NGTEVALLKS48 GIGKVAAALG 58 ATLLLEHCKP68 DVIINTGSAG78 GLAPTLKVGD88 IVVSDEARYH98 DADVTAFGYE 108 YGQLPGCPAG118 FKADDKLIAA128 AEACIAELNL138 NAVRGLIVSG148 DAFINGSVGL 158 AKIRHNFPQA168 IAVEMEATAI178 AHVCHNFNVP188 FVVVRAISDV198 ADQQSHLSFD 208 EFLAVAAKQS218 SLMVESLVQK228 LAHG
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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 .MTM or .MTM2 or .MTM3 or :3MTM;style chemicals stick;color identity;select .A:8 or .A:9 or .A:12 or .A:50 or .A:76 or .A:77 or .A:78 or .A:150 or .A:151 or .A:152 or .A:171 or .A:172 or .A:173 or .A:174 or .A:193 or .A:196 or .A:197 or .A:199 or .A:203 or .A:207; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: (3R,4S)-1-[(4-Amino-5H-pyrrolo[3,2-D]pyrimidin-7-YL)methyl]-4-[(methylsulfanyl)methyl]pyrrolidin-3-OL | Ligand Info | |||||
| Structure Description | Cyrstal structure of MTA/AdoHcy nucleosidase complexed with MT-DADMe-ImmA | PDB:1Y6Q | ||||
| Method | X-ray diffraction | Resolution | 2.20 Å | Mutation | No | [5] |
| PDB Sequence |
FSMKIGIIGA
8 MEEEVTLLRD18 KIENRQTISL28 GGCEIYTGQL38 NGTEVALLKS48 GIGKVAAALG 58 ATLLLEHCKP68 DVIINTGSAG78 GLAPTLKVGD88 IVVSDEARYH98 DADVTAFGYE 108 YGQLPGCPAG118 FKADDKLIAA128 AEACIAELNL138 NAVRGLIVSG148 DAFINGSVGL 158 AKIRHNFPQA168 IAVEMEATAI178 AHVCHNFNVP188 FVVVRAISDV198 ADQQSHLSFD 208 EFLAVAAKQS218 SLMVESLVQK228 LAHG
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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 .TDI or .TDI2 or .TDI3 or :3TDI;style chemicals stick;color identity;select .A:8 or .A:9 or .A:12 or .A:50 or .A:76 or .A:77 or .A:78 or .A:150 or .A:151 or .A:152 or .A:171 or .A:172 or .A:173 or .A:174 or .A:193 or .A:196 or .A:197 or .A:199 or .A:203 or .A:207; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: (3s,4r)-1-[(4-Amino-5h-Pyrrolo[3,2-D]pyrimidin-7-Yl)methyl]-4-[(Methylsulfanyl)methyl]pyrrolidin-3-Ol | Ligand Info | |||||
| Structure Description | Crystal structure of Escherichia coli 5'-methylthioadenosine/S-adenosyl homocysteine nucleosidase (MTAN) complexed with (3S,4R)-methylthio-DADMe-Immucillin-A | PDB:4YML | ||||
| Method | X-ray diffraction | Resolution | 1.75 Å | Mutation | No | [6] |
| PDB Sequence |
MKIGIIGAME
10 EEVTLLRDKI20 ENRQTISLGG30 CEIYTGQLNG40 TEVALLKSGI50 GKVAAALGAT 60 LLLEHCKPDV70 IINTGSAGGL80 APTLKVGDIV90 VSDEARYHDA100 DVTAFGYEYG 110 QLPGCPAGFK120 ADDKLIAAAE130 ACIAELNLNA140 VRGLIVSGDA150 FINGSVGLAK 160 IRHNFPQAIA170 VEMEATAIAH180 VCHNFNVPFV190 VVRAISDVAD200 QQSHLSFDEF 210 LAVAAKQSSL220 MVESLVQKLA230 H
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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 .4F0 or .4F02 or .4F03 or :34F0;style chemicals stick;color identity;select .A:8 or .A:9 or .A:12 or .A:50 or .A:76 or .A:77 or .A:78 or .A:150 or .A:151 or .A:152 or .A:171 or .A:172 or .A:173 or .A:174 or .A:193 or .A:196 or .A:197 or .A:199 or .A:203 or .A:207; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Structure of E. coli 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase reveals similarity to the purine nucleoside phosphorylases. Structure. 2001 Oct;9(10):941-53. | ||||
| REF 2 | Structure of Escherichia coli 5'-methylthioadenosine/ S-adenosylhomocysteine nucleosidase inhibitor complexes provide insight into the conformational changes required for substrate binding and catalysis. J Biol Chem. 2003 Mar 7;278(10):8761-70. | ||||
| REF 3 | Structural snapshots of MTA/AdoHcy nucleosidase along the reaction coordinate provide insights into enzyme and nucleoside flexibility during catalysis. J Mol Biol. 2005 Sep 23;352(3):559-74. | ||||
| REF 4 | Crystal structure of E. coli MTA/SAH nucleosidase in complex with (4-Chlorophenyl)thio-DADMe-ImmA | ||||
| REF 5 | Structural rationale for the affinity of pico- and femtomolar transition state analogues of Escherichia coli 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase. J Biol Chem. 2005 May 6;280(18):18274-82. | ||||
| REF 6 | Tight binding enantiomers of pre-clinical drug candidates. Bioorg Med Chem. 2015 Sep 1;23(17):5326-33. | ||||
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