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Mtb tmk in complex with compound 36

Analyse Mtb tmk in complex with compound 36 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4UNQ
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: H6D, NA
Pockets: 3 · best druggability 0.63

Structure

x-ray diffraction · 2 distinct chains · 54% 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	54% helix, 13% strand	F2GKC3

Ligands and binding sites

H6D · 4-[(R)-methylsulfinyl]-2-oxo-6-[3-(trifluoromethoxy)phenyl]-1,2-dihydropyridine-3-carbonitrile · ligand · 2 copies · chains A, B
NA · Sodium ion · metal · chains 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	200	0.63	0.83	23	H6D
2	193	0.61	0.82	22	H6D
3	119	0.39	0.74	20	empty

Interfaces

1 interface between chains.

A–B · 877 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

4UNQ · Mtb TMK in complex with compound 36 · 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 4UNQ · PDBe 4UNQ · UniProt F2GKC3

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