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Structure of PDB 5tmp Chain A Binding Site BS01

Receptor Information >5tmp Chain A (length=210) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure] RSKYIVIEGLEGAGKTTARNVVVETLEQLGIRDMVFTREPGGTQLAEKLR SLLLDIKSVGDEVITDKAEVLMFYAARVQLVETVIKPALANGTWVIGDRH DLSTQAYQGGGRGIDQHMLATLRDAVLGDFRPDLTLYLDVTPEVGLKRAR ARGELDRIEQESFDFFNRTRARYLELAAQDKSIHTIDATQPLEAVMDAIR TTVTHWVKEL

Ligand information Ligand ID Z5A InChI InChI=1S/C20H29N10O22P5/c1-8-3-29(20(34)26-18(8)33)12-2-9(27-28-22)10(47-12)4-45-53(35,36)49-55(39,40)51-57(43,44)52-56(41,42)50-54(37,38)46-5-11-14(31)15(32)19(48-11)30-7-25-13-16(21)23-6-24-17(13)30/h3,6-7,9-12,14-15,19,31-32H,2,4-5H2,1H3,(H,35,36)(H,37,38)(H,39,40)(H,41,42)(H,43,44)(H2,21,23,24)(H,26,33,34)/p-5/t9-,10+,11+,12+,14+,15+,19+/m0/s1 InChIKey QNIWSXQXLJIUJW-SLFMBYJQSA-I SMILES Software SMILES OpenEye OEToolkits 1.7.2 CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)([O-])OP(=O)([O-])OP(=O)([O-])OP(=O)([O-])OP(=O)([O-])OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)N=[N+]=[N-] CACTVS 3.370 CC1=CN([C@H]2C[C@H](N=[N+]=[N-])[C@@H](CO[P]([O-])(=O)O[P]([O-])(=O)O[P]([O-])(=O)O[P]([O-])(=O)O[P]([O-])(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)O2)C(=O)NC1=O CACTVS 3.370 CC1=CN([CH]2C[CH](N=[N+]=[N-])[CH](CO[P]([O-])(=O)O[P]([O-])(=O)O[P]([O-])(=O)O[P]([O-])(=O)O[P]([O-])(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)O2)C(=O)NC1=O OpenEye OEToolkits 1.7.2 CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)([O-])OP(=O)([O-])OP(=O)([O-])OP(=O)([O-])OP(=O)([O-])OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)N=[N+]=[N-] Formula C20 H24 N10 O22 P5 Name P1-(5'-ADENOSYL)P5-(5'-(3'AZIDO-3'-DEOXYTHYMIDYL))PENTAPHOSPHATE ChEMBL DrugBank DB03845 ZINC PDB chain 5tmp Chain A Residue 214 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure Global view Local view Structure summary [Spin on] [Spin off] [Reset] [High quality] [Low quality] [White background] [Black background] [Spin on] [Spin off] [Reset] [High quality] [Low quality] [White background] [Black background] PDB 5tmp Structural basis for efficient phosphorylation of 3'-azidothymidine monophosphate by Escherichia coli thymidylate kinase. Resolution 1.98 Å Binding residue (original residue number in PDB) E12 G13 G15 K16 T17 E40 R51 F74 R100 S104 T105 Y108 Q109 R149 R153 I159 Binding residue (residue number reindexed from 1) E11 G12 G14 K15 T16 E39 R50 F73 R99 S103 T104 Y107 Q108 R148 R152 I158 Annotation score 2 Binding affinity MOAD: Kd=34nM PDBbind-CN: -logKd/Ki=7.47,Kd=34nM

Enzymatic activity Enzyme Commision number 2.7.4.9: dTMP kinase.

Gene Ontology Molecular Function GO:0004798 thymidylate kinase activity GO:0005524 ATP binding GO:0016301 kinase activity GO:0042803 protein homodimerization activity

	Biological Process
GO:0006227	dUDP biosynthetic process
GO:0006233	dTDP biosynthetic process
GO:0006235	dTTP biosynthetic process
GO:0009165	nucleotide biosynthetic process
GO:0015949	nucleobase-containing small molecule interconversion
GO:0016310	phosphorylation
GO:0046940	nucleoside monophosphate phosphorylation

	Cellular Component
GO:0005737	cytoplasm
GO:0005829	cytosol

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