Structure of PDB 4fmb Chain D Binding Site BS02

Receptor Information
>4fmb Chain D (length=171) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PEYDALFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIEL
DGKTIKLQIWDTAGQERFRTITSSYYRGAHGIIVVYDVTDQESFNNVKQW
LQEIDRYASENVNKLLVGNKCDLTTKKVVDYTTAKEFADSLGIPFLETSA
KNATNVEQSFMTMAAEIKKRM
Ligand information
Ligand IDGDP
InChIInChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyQGWNDRXFNXRZMB-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(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)[C@@H](O)[C@H]3O
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
FormulaC10 H15 N5 O11 P2
NameGUANOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL384759
DrugBankDB04315
ZINCZINC000008215481
PDB chain4fmb Chain D Residue 202 [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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PDB4fmb Structurally Distinct Bacterial TBC-like GAPs Link Arf GTPase to Rab1 Inactivation to Counteract Host Defenses.
Resolution3.2 Å
Binding residue
(original residue number in PDB)		G21 V22 G23 K24 S25 C26 Y36 N124 K125 D127 L128 S154 A155 K156
Binding residue
(residue number reindexed from 1)		G16 V17 G18 K19 S20 C21 Y31 N119 K120 D122 L123 S149 A150 K151
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) Q70
Catalytic site (residue number reindexed from 1) Q65
Enzyme Commision number 3.6.5.2: small monomeric GTPase.
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0005525 GTP binding

View graph for
Molecular Function
External links
PDB RCSB:4fmb, PDBe:4fmb, PDBj:4fmb
PDBsum4fmb
PubMed22939626
UniProtP62820|RAB1A_HUMAN Ras-related protein Rab-1A (Gene Name=RAB1A)

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