Structure of PDB 7kdc Chain B Binding Site BS01

Receptor Information
>7kdc Chain B (length=180) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VRSVKVVLVGDGGCGKTSLLMVFADGAFPESYTPTVFERYMVNLQVKGKP
VHLHIWDTAGLDDYDRLRPLFYPDASVLLLCFDVTSPNSFDNIFNRWYPE
VNHFCKKVPIIVVGCKTDLRKDKSLVNKLRRNGLEPVTYHRGQEMARSVG
AVAYLECSARLHDNVHAVFQEAAEVALSSR
Ligand information
Ligand IDGNP
InChIInChI=1S/C10H17N6O13P3/c11-10-13-7-4(8(19)14-10)12-2-16(7)9-6(18)5(17)3(28-9)1-27-32(25,26)29-31(23,24)15-30(20,21)22/h2-3,5-6,9,17-18H,1H2,(H,25,26)(H3,11,13,14,19)(H4,15,20,21,22,23,24)/t3-,5-,6-,9-/m1/s1
InChIKeyUQABYHGXWYXDTK-UUOKFMHZSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
FormulaC10 H17 N6 O13 P3
NamePHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
ChEMBLCHEMBL1233085
DrugBankDB02082
ZINCZINC000037868676
PDB chain7kdc Chain B Residue 201 [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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PDB7kdc A putative structural mechanism underlying the antithetic effect of homologous RND1 and RhoD GTPases in mammalian plexin regulation.
Resolution3.1 Å
Binding residue
(original residue number in PDB)		G26 G27 G29 K30 T31 S32 F42 Y46 T49 G74 K130 D132 L133 A173 R174
Binding residue
(residue number reindexed from 1)		G12 G13 G15 K16 T17 S18 F28 Y32 T35 G60 K116 D118 L119 A159 R160
Annotation score3
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0005525 GTP binding
Biological Process
GO:0007264 small GTPase-mediated signal transduction

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:7kdc, PDBe:7kdc, PDBj:7kdc
PDBsum7kdc
PubMed34114565
UniProtO00212|RHOD_HUMAN Rho-related GTP-binding protein RhoD (Gene Name=RHOD)

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