Structure of PDB 5knq Chain D Binding Site BS01

Receptor Information
>5knq Chain D (length=181) Species: 83332 (Mycobacterium tuberculosis H37Rv) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GDIKSVLLTAEQIQARIAELGEQIGNDYRELSATTGQDLLLITVLKGAVL
FVTDLARAIPVPTQFEFMAVSSYGSSTSSSGVVRILKDLDRDIHGRDVLI
VEDVVDSGLTLSWLSRNLTSRNPRSLRVCTLLRKPDAVHANVEIAYVGFD
IPNDFVVGYGLDYDERYRDLSYIGTLDPRVY
Ligand information
Ligand ID6W8
InChIInChI=1S/C10H15N6O5P/c11-10-14-8-7(9(17)15-10)13-3-16(8)5-1-12-2-6(5)21-4-22(18,19)20/h3,5-6,12H,1-2,4H2,(H2,18,19,20)(H3,11,14,15,17)/t5-,6+/m1/s1
InChIKeyLMOOKHOOULQCAZ-RITPCOANSA-N
SMILES
SoftwareSMILES
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3CNC[CH]3OC[P](O)(O)=O
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[C@@H]3CNC[C@@H]3OC[P](O)(O)=O
OpenEye OEToolkits 2.0.5c1nc2c(n1[C@@H]3CNC[C@@H]3OCP(=O)(O)O)N=C(NC2=O)N
OpenEye OEToolkits 2.0.5c1nc2c(n1C3CNCC3OCP(=O)(O)O)N=C(NC2=O)N
FormulaC10 H15 N6 O5 P
Name[(3~{S},4~{R})-4-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)pyrrolidin-3-yl]oxymethylphosphonic acid;
[3S,4R]-(4-(Guanin-9-yl)pyrrolidin-3-yl)oxymethanephosphonic acid
ChEMBLCHEMBL4283940
DrugBank
ZINC
PDB chain5knq Chain D 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]
PDB5knq Crystal structure of Mycobacterium tuberculosis hypoxanthine guanine phosphoribosyltransferase in complex with pyrrolidine nucleoside phosphonate
Resolution2.553 Å
Binding residue
(original residue number in PDB)
D126 S127 G128 K154 F175 V176 L181 D182
Binding residue
(residue number reindexed from 1)
D106 S107 G108 K134 F155 V156 L161 D162
Annotation score1
Binding affinityBindingDB: Ki=8000nM
Enzymatic activity
Catalytic site (original residue number in PDB) E122 D123 D126 F175 R188
Catalytic site (residue number reindexed from 1) E102 D103 D106 F155 R168
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:0016757 glycosyltransferase activity
GO:0046872 metal ion binding
GO:0052657 guanine phosphoribosyltransferase activity
Biological Process
GO:0006166 purine ribonucleoside salvage
GO:0006177 GMP biosynthetic process
GO:0006178 guanine salvage
GO:0006188 IMP biosynthetic process
GO:0032263 GMP salvage
GO:0032264 IMP salvage
GO:0043101 purine-containing compound salvage
GO:0046100 hypoxanthine metabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component
External links
PDB RCSB:5knq, PDBe:5knq, PDBj:5knq
PDBsum5knq
PubMed
UniProtP9WHQ9|HGPRT_MYCTU Hypoxanthine-guanine phosphoribosyltransferase (Gene Name=hpt)

[Back to BioLiP]