Structure of PDB 4qrh Chain B Binding Site BS01

Receptor Information
>4qrh Chain B (length=186) Species: 1458279 (Staphylococcus aureus USA300-ISMMS1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DNEKGLLIVLSGPSGVGKGTVRKRIFEDPSTSYKYSISMTTRQMREGEVD
GVDYFFKTRDAFEALIKDDQFIEYAEYVGNYYGTPVQYVKDTMDEGHDVF
LEIEVEGAKQVRKKFPDALFIFLAPPSLEHLNEARKEVEMMNLYDYVVVN
DEVELAKNRIQCIVEAEHLKRERVEAKYRKMILEAK
Ligand information
Ligand ID0O2
InChIInChI=1S/C10H18N5O20P5/c11-10-13-7-4(8(17)14-10)12-2-15(7)9-5(16)6(32-39(26,27)33-36(18,19)20)3(31-9)1-30-38(24,25)35-40(28,29)34-37(21,22)23/h2-3,5-6,9,16H,1H2,(H,24,25)(H,26,27)(H,28,29)(H2,18,19,20)(H2,21,22,23)(H3,11,13,14,17)/t3-,5-,6-,9-/m1/s1
InChIKeyKCPMACXZAITQAX-UUOKFMHZSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3OP(=O)(O)OP(=O)(O)O
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)OP(=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O[P](O)(=O)O[P](O)(O)=O)[C@H]3O
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O[P](O)(=O)O[P](O)(O)=O)[CH]3O
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)OP(=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N
FormulaC10 H18 N5 O20 P5
Nameguanosine 5'-(tetrahydrogen triphosphate) 3'-(trihydrogen diphosphate)
ChEMBL
DrugBank
ZINCZINC000083923877
PDB chain4qrh Chain B Residue 303 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4qrh Molecular Mechanism and Evolution of Guanylate Kinase Regulation by (p)ppGpp.
Resolution1.65 Å
Binding residue
(original residue number in PDB)		G16 V17 G18 K19 S39 R43 Y55 E74 Y78 Y83 G84 E103 I104 E105
Binding residue
(residue number reindexed from 1)		G15 V16 G17 K18 S38 R42 Y54 E73 Y77 Y82 G83 E102 I103 E104
Annotation score3
Binding affinityMOAD: Ki=7uM
PDBbind-CN: -logKd/Ki=5.15,Ki=7.0uM
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
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4qrh, PDBe:4qrh, PDBj:4qrh
PDBsum4qrh
PubMed25661490
UniProtA0A0J9X1Z9

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