MolNFT v1 · #72561 · protein

X-ray structure of ketohexokinase in complex with a thieno pyridinol compound

3NCA: “X-ray structure of ketohexokinase in complex with a thieno pyridinol compound”. X-ray diffraction, 2 ligands (TR2, SO4), 6 pockets (best druggability 0.77). MolNFT v1 #72561 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 3NCA
Type: protein
Length: 597 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ketohexokinase
EC: 2.7.1.3
Ligands: TR2, SO4
Pockets: 6 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 36% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ketohexokinase (EC 2.7.1.3)	protein	296	35% helix, 25% strand	—
B	Ketohexokinase (EC 2.7.1.3)	protein	301	37% helix, 25% strand	—

Ligands and binding sites

TR2 · thieno[3,2-b]pyridin-7-ol · ligand · chains A
SO4 · Sulfate ion · ion · 3 copies · chains A, B

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

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	654	0.77	0.82	66	SO4, TR2
2	805	0.74	0.79	89	SO4
3	110	0.48	0.80	23	empty
4	133	0.43	0.76	24	empty
5	66	0.32	0.76	14	empty

Interfaces

1 interface between chains.

A–B · 1652 Å² buried · 32 hydrogen bonds · protein-protein

Compared structures

3NCA · X-ray structure of ketohexokinase in complex with a thieno pyridinol compound · 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
Elsewhere: RCSB PDB 3NCA · PDBe 3NCA

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