Target Binding Site Detail
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T94400 | Target Info | |||
| Target Name | Mycobacterium Thymidine monophosphate kinase (MycB tmk) | ||||
| Synonyms | tmk; Thymidylic kinase; Thymidylic acid kinase; Thymidylate monophosphate kinase; Thymidylate kinase; Thymidine 5'-monophosphate kinase; TMPK; Deoxythymidine 5'-monophosphate kinase; DTMPkinase | ||||
| Target Type | Literature-reported Target | ||||
| Gene Name | MycB tmk | ||||
| Biochemical Class | Kinase | ||||
| UniProt ID | |||||
| Ligand General Information | Top | ||||
|---|---|---|---|---|---|
| Ligand Name | Thymidine-5'-Phosphate | Ligand Info | |||
| Canonical SMILES | CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)O)O | ||||
| InChI | 1S/C10H15N2O8P/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(20-8)4-19-21(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1 | ||||
| InChIKey | GYOZYWVXFNDGLU-XLPZGREQSA-N | ||||
| PubChem Compound ID | 9700 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 1GSI CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE MONOPHOSPHATE (TMP) | ||||||
| Method | X-ray diffraction | Resolution | 1.60 Å | Mutation | No | [1] |
| PDB Sequence |
MLIAIEGVDG
10 AGKRTLVEKL20 SGAFRAAGRS30 VATLAFPRYG40 QSVAADIAAE50 ALHGEHGDLA 60 SSVYAMATLF70 ALDRAGAVHT80 IQGLCRGYDV90 VILDRYVASN100 AAYSAARLHE 110 NAAGKAAAWV120 QRIEFARLGL130 PKPDWQVLLA140 VSAELAGERS150 RGRAQRDPGR 160 ARDNYERDAE170 LQQRTGAVYA180 ELAAQGWGGR190 WLVVGADVDP200 GRLAATLA |
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| PDB ID: 1N5I CRYSTAL STRUCTURE OF INACTIVE MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE MONOPHOSPHATE (TMP) AT PH 4.6 (RESOLUTION 1.85 A) | ||||||
| Method | X-ray diffraction | Resolution | 1.85 Å | Mutation | No | [2] |
| PDB Sequence |
MLIAIEGVDG
10 AGKRTLVEKL20 SGAFRAAGRS30 VATLAFPRYG40 QSVAADIAAE50 ALHGEHGDLA 60 SSVYAMATLF70 ALDRAGAVHT80 IQGLCRGYDV90 VILDRYVASN100 AAYSAARLHE 110 NAAGKAAAWV120 QRIEFARLGL130 PKPDWQVLLA140 VSAELAGERS150 RGRAQRDPGR 160 ARDNYERDAE170 LQQRTGAVYA180 ELAAQGWGGR190 WLVVGADVDP200 GRLAATLA |
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| PDB ID: 1G3U CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE MONOPHOSPHATE (TMP) | ||||||
| Method | X-ray diffraction | Resolution | 1.95 Å | Mutation | No | [3] |
| PDB Sequence |
MLIAIEGVDG
10 AGKRTLVEKL20 SGAFRAAGRS30 VATLAFPRYG40 QSVAADIAAE50 ALHGEHGDLA 60 SSVYAMATLF70 ALDRAGAVHT80 IQGLCRGYDV90 VILDRYVASN100 AAYSAARLHE 110 NAAGKAAAWV120 QRIEFARLGL130 PKPDWQVLLA140 VSAELAGERS150 RGRAQRDPGR 160 ARDNYERDAE170 LQQRTGAVYA180 ELAAQGWGGR190 WLVVGADVDP200 GRLAATLA |
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| PDB ID: 1N5K CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE CRYSTALLIZED IN SODIUM MALONATE (RESOLUTION 2.1 A) | ||||||
| Method | X-ray diffraction | Resolution | 2.10 Å | Mutation | No | [2] |
| PDB Sequence |
MLIAIEGVDG
10 AGKRTLVEKL20 SGAFRAAGRS30 VATLAFPRYG40 QSVAADIAAE50 ALHGEHGDLA 60 SSVYAMATLF70 ALDRAGAVHT80 IQGLCRGYDV90 VILDRYVASN100 AAYSAARLHE 110 NAAGKAAAWV120 QRIEFARLGL130 PKPDWQVLLA140 VSAELAGERR162 DNYERDAELQ 172 QRTGAVYAEL182 AAQGWGGRWL192 VVGADVDPGR202 LAATLA
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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 .TMP or .TMP2 or .TMP3 or :3TMP;style chemicals stick;color identity;select .A:9 or .A:13 or .A:36 or .A:37 or .A:39 or .A:52 or .A:70 or .A:74 or .A:95 or .A:96 or .A:99 or .A:100 or .A:103 or .A:163 or .A:165; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 1N5L CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE CRYSTALLIZED IN SODIUM MALONATE, AFTER CATALYSIS IN THE CRYSTAL (2.3 A RESOLUTION) | ||||||
| Method | X-ray diffraction | Resolution | 2.30 Å | Mutation | No | [2] |
| PDB Sequence |
MLIAIEGVDG
10 AGKRTLVEKL20 SGAFRAAGRS30 VATLAFPRYG40 QSVAADIAAE50 ALHGEHGDLA 60 SSVYAMATLF70 ALDRAGAVHT80 IQGLCRGYDV90 VILDRYVASN100 AAYSAARLHE 110 NAAGKAAAWV120 QRIEFARLGL130 PKPDWQVLLA140 VSAELAGERD163 NYERDAELQQ 173 RTGAVYAELA183 AQGWGGRWLV193 VGADVDPGRL203 AATLA
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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 .TMP or .TMP2 or .TMP3 or :3TMP;style chemicals stick;color identity;select .A:36 or .A:37 or .A:39 or .A:52 or .A:70 or .A:74 or .A:95 or .A:96 or .A:99 or .A:100 or .A:103 or .A:124 or .A:163 or .A:165; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Cryophotolysis of caged compounds: a technique for trapping intermediate states in protein crystals. Acta Crystallogr D Biol Crystallogr. 2002 Apr;58(Pt 4):607-14. | ||||
| REF 2 | Mycobacterium tuberculosis thymidylate kinase: structural studies of intermediates along the reaction pathway. J Mol Biol. 2003 Apr 11;327(5):1077-92. | ||||
| REF 3 | X-ray structure of TMP kinase from Mycobacterium tuberculosis complexed with TMP at 1.95 A resolution. J Mol Biol. 2001 Aug 3;311(1):87-100. | ||||
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