MolNFT v1 · #107812 · protein

Mtb tmk in complex with compound 40

4UNS · Thymidylate kinase: “Mtb tmk in complex with compound 40”. X-ray diffraction, 2 ligands (QZ3, NA), 3 pockets (best druggability 0.61). MolNFT v1 #107812 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4UNS
Type: protein
Length: 374 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thymidylate kinase
EC: 2.7.4.9
UniProt: F2GKC3
Ligands: QZ3, NA
Pockets: 3 · best druggability 0.61

Structure

x-ray diffraction · 2 distinct chains · 53% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Thymidylate kinase (EC 2.7.4.9)	protein	186	54% helix, 13% strand	F2GKC3
B	Thymidylate kinase (EC 2.7.4.9)	protein	188	53% helix, 13% strand	F2GKC3

Ligands and binding sites

QZ3 · N-[4-(3-cyano-7-ethyl-5-methyl-2-oxo-1H-1,6-naphthyridin-4-yl)phenyl]methanesulfonamide · ligand · 2 copies · chains A, B
NA · Sodium ion · metal · 2 copies · chains A, B

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

Pockets

3 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	185	0.61	0.82	21	QZ3
2	171	0.61	0.83	20	QZ3
3	125	0.36	0.73	19	empty

Interfaces

1 interface between chains.

A–B · 855 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

4UNS · Mtb TMK in complex with compound 40 · 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 F2GKC3
Elsewhere: RCSB PDB 4UNS · PDBe 4UNS · UniProt F2GKC3

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