Structure of PDB 2f3r Chain B Binding Site BS01

Receptor Information
>2f3r Chain B (length=199) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AQGTLYIVSAPSGAGKSSLIQALLKTQPLYDTQVSVSHTTRQPRPGEVHG
EHYFFVNHDEFKEMISRDAFLEHAEVFGNYYGTSREAIEQVLATGVDVFL
DIDWQGAQQIRQKMPHARSIFILPPSKIELDRRLRGSEEVIAKRMAQAVA
EMSHYAEYDYLIVNDDFDTALTDLKTIIRAERLRMSRQKQRHDALISKL
Ligand information
Ligand IDG5P
InChIInChI=1S/C20H29N10O23P5/c21-14-8-15(24-3-23-14)29(4-25-8)18-12(33)10(31)6(48-18)1-46-54(36,37)50-56(40,41)52-58(44,45)53-57(42,43)51-55(38,39)47-2-7-11(32)13(34)19(49-7)30-5-26-9-16(30)27-20(22)28-17(9)35/h3-7,10-13,18-19,31-34H,1-2H2,(H,36,37)(H,38,39)(H,40,41)(H,42,43)(H,44,45)(H2,21,23,24)(H3,22,27,28,35)/t6-,7-,10-,11-,12-,13-,18-,19-/m1/s1
InChIKeyCNMILLPGDWDFCZ-INFSMZHSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)[CH](O)[CH]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)O[P@@](=O)(O)O[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5N=C(NC6=O)N)O)O)O)O)N
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5N=C(NC6=O)N)O)O)O)O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[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]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)[C@@H](O)[C@H]3O
FormulaC20 H29 N10 O23 P5
NameP1-(5'-ADENOSYL)-P5-(5'-GUANOSYL) PENTAPHOSPHATE
ChEMBL
DrugBank
ZINCZINC000261495500
PDB chain2f3r Chain B Residue 602 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB2f3r Crystal structures of GMP kinase in complex with ganciclovir monophosphate and Ap5G.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		G14 G16 K17 S18 S19 S38 R42 R45 Y54 E73 Y82 G83 D102 I103 D104 G107 R134 G137
Binding residue
(residue number reindexed from 1)		G13 G15 K16 S17 S18 S37 R41 R44 Y53 E72 Y81 G82 D101 I102 D103 G106 R133 G136
Annotation score3
Binding affinityMOAD: ic50=0.5uM
Enzymatic activity
Enzyme Commision number 2.7.4.8: guanylate kinase.
Gene Ontology
Molecular Function
GO:0004385 guanylate kinase activity
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0042802 identical protein binding
Biological Process
GO:0006163 purine nucleotide metabolic process
GO:0016310 phosphorylation
GO:0046037 GMP metabolic process
GO:0046710 GDP metabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2f3r, PDBe:2f3r, PDBj:2f3r
PDBsum2f3r
PubMed16690197
UniProtP60546|KGUA_ECOLI Guanylate kinase (Gene Name=gmk)

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