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The identification, analysis and structure-based development of novel inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase

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PDB: 4M5L
Type: protein
Length: 159 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
EC: 2.7.6.3
UniProt: P26281
Ligands: APC, YH4, CA
Pockets: 1 · best druggability 0.62

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase (EC 2.7.6.3)	protein	159	30% helix, 27% strand	P26281

Ligands and binding sites

APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · chains A
YH4 · 2-amino-8-{[2-(2-methylphenyl)-2-oxoethyl]sulfanyl}-1,7-dihydro-6H-purin-6-one · ligand · chains A
CA · Calcium ion · metal · 3 copies · chains A
GOL · Glycerol · additive · chains A

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	326	0.62	0.79	41	APC, CA, GOL, YH4

Compared structures

4M5L · The Identification, Analysis and Structure-Based Development of Novel Inhibitors of… · the same entry in another collection · chain A against A, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P26281
Elsewhere: RCSB PDB 4M5L · PDBe 4M5L · UniProt P26281

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