MolNFT v1 · #72428 · protein

Crystal structure of 3-dehydroquinate dehydratase from mycobacterium tuberculosis in complex with inhibitor 3

3N87: “Crystal structure of 3-dehydroquinate dehydratase from mycobacterium tuberculosis in complex with inhibitor 3”. X-ray diffraction, 1 ligand (N87), 20 pockets (best druggability 0.78). MolNFT v1 #72428 on GenesisL1: 3D structure…

PDB: 3N87
Type: protein
Length: 3,384 residues
Chains: 24
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3-dehydroquinate dehydratase
EC: 4.2.1.10
UniProt: P0A4Z6
Ligands: N87
Pockets: 20 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 45% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X	3-dehydroquinate dehydratase (EC 4.2.1.10)	protein	141	45% helix, 17% strand	P0A4Z6

Ligands and binding sites

N87 · (1R,4R,5R)-1,4,5-trihydroxy-3-[3-(phenylcarbonyl)phenyl]cyclohex-2-ene-1-carboxylic acid · ligand · 24 copies · chains A, L, B, E, C, D, G, F, H, J, I, K, M, X, N, Q, O, P, S, R, T, V, U, W

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	169	0.78	0.94	29	N87
2	224	0.78	0.92	31	N87
3	188	0.78	0.93	30	N87
4	197	0.77	0.93	31	N87
5	203	0.77	0.92	28	N87

Interfaces

36 interfaces between chains.

E–K · 1018 Å² buried · 14 hydrogen bonds · protein-protein
P–U · 1005 Å² buried · 16 hydrogen bonds · protein-protein
B–F · 1004 Å² buried · 15 hydrogen bonds · protein-protein
V–X · 1003 Å² buried · 17 hydrogen bonds · protein-protein
C–H · 996 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

3N87 · Crystal structure of 3-dehydroquinate dehydratase from Mycobacterium tuberculosis in… · 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 P0A4Z6
Elsewhere: RCSB PDB 3N87 · PDBe 3N87 · UniProt P0A4Z6

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