Structure of PDB 4rab Chain B Binding Site BS01

Receptor Information
>4rab Chain B (length=201) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SPGVVISDDEPGYDLDLFCIPNHYAEDLERVFIPHGLIMDRTERLARDVM
KEMGGHHIVALCVLKGGYKFFADLLDYIKALNRNSDRSPMTVDFIRLKSK
VIGGDDLSTLTGKNVLIVEDIIDTGKTMQTLLSLVRQYNPKMVKVASLLV
KRTPRSYKPDFVGFEIPDKFVVGYALDYNEYFRDLNHVCVISETGKAKYK
A
Ligand information
Ligand ID3L3
InChIInChI=1S/C13H19BrN6O8P2/c14-12-16-9-10(17-13(15)18-11(9)21)20(12)2-1-19(4-7-29(22,23)24)3-5-28-6-8-30(25,26)27/h4,6-8H,1-3,5H2,(H2,22,23,24)(H2,25,26,27)(H3,15,17,18,21)/b7-4+,8-6+
InChIKeyPVMQSKKLLHWGSB-IJYBVRAASA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6C(CN(CCO/C=C/P(=O)(O)O)/C=C/P(=O)(O)O)n1c2c(nc1Br)C(=O)NC(=N2)N
ACDLabs 12.01O=P(O)(O)/C=C/N(CCO/C=C/P(=O)(O)O)CCn1c2N=C(NC(=O)c2nc1Br)N
CACTVS 3.385NC1=Nc2n(CCN(CCO/C=C/[P](O)(O)=O)\C=C\[P](O)(O)=O)c(Br)nc2C(=O)N1
CACTVS 3.385NC1=Nc2n(CCN(CCOC=C[P](O)(O)=O)C=C[P](O)(O)=O)c(Br)nc2C(=O)N1
OpenEye OEToolkits 1.7.6C(CN(CCOC=CP(=O)(O)O)C=CP(=O)(O)O)n1c2c(nc1Br)C(=O)NC(=N2)N
FormulaC13 H19 Br N6 O8 P2
Name[(E)-2-(2-{[2-(2-amino-8-bromo-6-oxo-1,6-dihydro-9H-purin-9-yl)ethyl][(E)-2-phosphonoethenyl]amino}ethoxy)ethenyl]phosphonic acid
ChEMBL
DrugBank
ZINCZINC000263620911
PDB chain4rab Chain B Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure 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]
PDB4rab Aza-acyclic Nucleoside Phosphonates Containing a Second Phosphonate Group As Inhibitors of the Human, Plasmodium falciparum and vivax 6-Oxopurine Phosphoribosyltransferases and Their Prodrugs As Antimalarial Agents.
Resolution2.264 Å
Binding residue
(original residue number in PDB)		I135 D137 T138 G139 T141 K165 F186 V187 D193
Binding residue
(residue number reindexed from 1)		I121 D123 T124 G125 T127 K151 F170 V171 D177
Annotation score1
Binding affinityMOAD: Ki=0.04uM
Enzymatic activity
Catalytic site (original residue number in PDB) E133 D134 D137 F186 R199
Catalytic site (residue number reindexed from 1) E119 D120 D123 F170 R183
Enzyme Commision number 2.4.2.8: hypoxanthine phosphoribosyltransferase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0000287 magnesium ion binding
GO:0004422 hypoxanthine phosphoribosyltransferase activity
GO:0005515 protein binding
GO:0016757 glycosyltransferase activity
GO:0042802 identical protein binding
GO:0046872 metal ion binding
GO:0052657 guanine phosphoribosyltransferase activity
Biological Process
GO:0001913 T cell mediated cytotoxicity
GO:0001975 response to amphetamine
GO:0006164 purine nucleotide biosynthetic process
GO:0006166 purine ribonucleoside salvage
GO:0006178 guanine salvage
GO:0007625 grooming behavior
GO:0007626 locomotory behavior
GO:0021756 striatum development
GO:0021895 cerebral cortex neuron differentiation
GO:0021954 central nervous system neuron development
GO:0032263 GMP salvage
GO:0032264 IMP salvage
GO:0042417 dopamine metabolic process
GO:0043103 hypoxanthine salvage
GO:0044209 AMP salvage
GO:0045964 positive regulation of dopamine metabolic process
GO:0046038 GMP catabolic process
GO:0046040 IMP metabolic process
GO:0046083 adenine metabolic process
GO:0046100 hypoxanthine metabolic process
GO:0046651 lymphocyte proliferation
GO:0048813 dendrite morphogenesis
GO:0051289 protein homotetramerization
GO:0071542 dopaminergic neuron differentiation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0070062 extracellular exosome

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4rab, PDBe:4rab, PDBj:4rab
PDBsum4rab
PubMed25494538
UniProtP00492|HPRT_HUMAN Hypoxanthine-guanine phosphoribosyltransferase (Gene Name=HPRT1)

[Back to BioLiP]