MolNFT v1 · #119594 · protein

Inha in complex with a DNA encoded library hit

5G0V · Enoyl-acyl carrier protein reductase: “Inha in complex with a DNA encoded library hit”. X-ray diffraction, 3 ligands (NAD, JDD, MG), 12 pockets (best druggability 0.83). MolNFT v1 #119594 on GenesisL1: 3D structure, binding sites…

PDB: 5G0V
Type: protein
Length: 1,025 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Enoyl-acyl carrier protein reductase
EC: 1.3.1.9
UniProt: P9WGR1
Ligands: NAD, JDD, MG
Pockets: 12 · best druggability 0.83

Structure

x-ray diffraction · 4 distinct chains · 45% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Enoyl-acyl carrier protein reductase (EC 1.3.1.9)	protein	260	44% helix, 17% strand	P9WGR1
B	Enoyl-acyl carrier protein reductase (EC 1.3.1.9)	protein	258	46% helix, 17% strand	P9WGR1
C	Enoyl-acyl carrier protein reductase (EC 1.3.1.9)	protein	244	43% helix, 18% strand	P9WGR1
D	Enoyl-acyl carrier protein reductase (EC 1.3.1.9)	protein	263	46% helix, 17% strand	P9WGR1

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
JDD · N-[2-(methylamino)-2-oxidanylidene-ethyl]-2-(4-pyrazol-1-ylphenyl)-N-(1-pyridin-2-ylpiperidin-4-yl)ethanamide · ligand · chains B
MG · Magnesium ion · metal · chains A

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

Pockets

12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1148	0.83	0.85	52	empty
2	568	0.78	0.84	48	NAD, JDD
3	620	0.75	0.81	52	NAD
4	486	0.71	0.80	50	NAD
5	499	0.71	0.80	46	NAD

Interfaces

6 interfaces between chains.

B–D · 1600 Å² buried · 21 hydrogen bonds · protein-protein
A–C · 1584 Å² buried · 20 hydrogen bonds · protein-protein
B–C · 1504 Å² buried · 18 hydrogen bonds · protein-protein
A–D · 1443 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 724 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

5G0V · InhA in complex with a DNA encoded library hit · the same entry in another collection · chain D against D, TM-score 1.00
P9WGR1 · AlphaFold monomer V2.0 prediction for enoyl-[acyl-carrier-protein] reductase [NADH]… · a predicted model of the same protein · chain C against A, TM-score 0.99

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 P9WGR1
Elsewhere: RCSB PDB 5G0V · PDBe 5G0V · UniProt P9WGR1

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