MolNFT v1 · #139006 · protein

PKM2 in complex with compound 5

5X1W · Pyruvate kinase pkm: “PKM2 in complex with compound 5”. X-ray diffraction, 2 ligands (FBP, 7Y0), 20 pockets (best druggability 0.88). MolNFT v1 #139006 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5X1W
Type: protein
Length: 2,048 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pyruvate kinase pkm
EC: 2.7.1.40
UniProt: P14618
Ligands: FBP, 7Y0
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 3 distinct chains · 40% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Pyruvate kinase pkm (EC 2.7.1.40)	protein	518	39% helix, 21% strand	P14618
B	Pyruvate kinase pkm (EC 2.7.1.40)	protein	501	40% helix, 20% strand	P14618
D	Pyruvate kinase pkm (EC 2.7.1.40)	protein	511	40% helix, 20% strand	P14618

Ligands and binding sites

FBP · 1,6-di-O-phosphono-beta-D-fructofuranose · ligand · 4 copies · chains A, B, C, D
7Y0 · 4-[2,3-bis(chloranyl)phenyl]carbonyl-N-[2-[[4-[2,3-bis(chloranyl)phenyl]carbonyl-1-methyl-pyrrol-2-yl]carbonylamino]ethyl]-1-methyl-pyrrole-2-carboxamide · ligand · 2 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	701	0.88	0.92	57	empty
2	343	0.87	0.96	43	7Y0
3	322	0.86	0.96	41	7Y0
4	769	0.79	0.83	89	empty
5	713	0.77	0.82	94	empty

Interfaces

6 interfaces between chains.

A–B · 2997 Å² buried · 41 hydrogen bonds · protein-protein
C–D · 2974 Å² buried · 41 hydrogen bonds · protein-protein
A–C · 1515 Å² buried · 26 hydrogen bonds · protein-protein
B–D · 1479 Å² buried · 23 hydrogen bonds · protein-protein
B–C · 41 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5X1W · PKM2 in complex with compound 5 · 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 P14618
Elsewhere: RCSB PDB 5X1W · PDBe 5X1W · UniProt P14618

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