MolNFT v1 · #138116 · protein

Human hgprt in complex with [(2-[(guanin-9-YL)METHYL]PROPANE-1,3- DIYL)BIS(OXY)]BIS(METHYLENE)DIPHOSPHONIC acid

5W8V · Hypoxanthine-guanine phosphoribosyltransferase: “Human hgprt in complex with [(2-[(guanin-9-YL)METHYL]PROPANE-1,3- DIYL)BIS(OXY)]BIS(METHYLENE)DIPHOSPHONIC…”. X-ray diffraction, 2 ligands (9YP, MG), 7 pockets (best druggability…

PDB: 5W8V
Type: protein
Length: 819 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hypoxanthine-guanine phosphoribosyltransferase
EC: 2.4.2.8
UniProt: P00492
Ligands: 9YP, MG
Pockets: 7 · best druggability 0.83

Structure

x-ray diffraction · 4 distinct chains · 30% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8)	protein	206	31% helix, 30% strand	P00492
B	Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8)	protein	204	30% helix, 31% strand	P00492
C	Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8)	protein	205	30% helix, 30% strand	P00492
D	Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8)	protein	204	31% helix, 29% strand	P00492

Ligands and binding sites

9YP · {[(2R)-2-[(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl) methyl]-3-(2-phosphonoethoxy)propoxy]methyl}phosphonic acid · ligand · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 4 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1154	0.83	0.85	99	empty
2	164	0.55	0.80	33	empty
3	275	0.55	0.76	39	9YP, MG
4	167	0.52	0.78	33	empty
5	205	0.47	0.74	26	9YP, MG

Interfaces

6 interfaces between chains.

B–D · 1707 Å² buried · 30 hydrogen bonds · protein-protein
A–C · 1698 Å² buried · 32 hydrogen bonds · protein-protein
C–D · 846 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 843 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 335 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

5W8V · HUMAN HGPRT in complex with [(2-[(guanin-9-yl)methyl]propane-1,3-diyl)bis(oxy)]bis(methyle… · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P00492
Elsewhere: RCSB PDB 5W8V · PDBe 5W8V · UniProt P00492

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