MolNFT v1 · #114509 · protein

Human hgprt in complex with (S)-hpephx, an acyclic nucleoside phosphonate

5BRN · Hypoxanthine-guanine phosphoribosyltransferase: “Human hgprt in complex with (S)-hpephx, an acyclic nucleoside phosphonate”. X-ray diffraction, 2 ligands (4X2, MG), 13 pockets (best druggability 0.83). MolNFT v1 #114509 on…

PDB: 5BRN
Type: protein
Length: 780 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: 4X2, MG
Pockets: 13 · best druggability 0.83

Structure

x-ray diffraction · 4 distinct chains · 31% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8)	protein	194	31% helix, 30% strand	P00492
B	Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8)	protein	194	32% helix, 30% strand	P00492
C	Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8)	protein	195	28% helix, 27% strand	P00492
D	Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8)	protein	197	31% helix, 29% strand	P00492

Ligands and binding sites

4X2 · (2-{[(2S)-1-hydroxy-3-(6-oxo-1,6-dihydro-9H-purin-9-yl)propan-2-yl]oxy}ethyl)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

13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1110	0.83	0.84	76	empty
2	181	0.61	0.82	31	empty
3	195	0.58	0.80	33	empty
4	153	0.54	0.80	32	empty
5	262	0.53	0.76	29	MG, 4X2

Interfaces

6 interfaces between chains.

A–D · 1556 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 1367 Å² buried · 14 hydrogen bonds · protein-protein
A–C · 842 Å² buried · 11 hydrogen bonds · protein-protein
B–D · 828 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 319 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

5BRN · Human HGPRT in complex with (S)-HPEPHx, an acyclic nucleoside phosphonate · 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 5BRN · PDBe 5BRN · UniProt P00492

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