MolNFT v1 · #100872 · protein

Inhibitors of 4-phosphopanthetheine adenylyltransferase (ppat)

4NAH · Phosphopantetheine adenylyltransferase: “Inhibitors of 4-phosphopanthetheine adenylyltransferase (ppat)”. X-ray diffraction, 2 ligands (AGS, 2VJ), 18 pockets (best druggability 0.84). MolNFT v1 #100872 on GenesisL1: 3D structure…

PDB: 4NAH
Type: protein
Length: 958 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phosphopantetheine adenylyltransferase
EC: 2.7.7.3
UniProt: P63820
Ligands: AGS, 2VJ
Pockets: 18 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 43% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Phosphopantetheine adenylyltransferase (EC 2.7.7.3)	protein	159	42% helix, 19% strand	P63820
B, C, E, F	Phosphopantetheine adenylyltransferase (EC 2.7.7.3)	protein	160	43% helix, 19% strand	P63820

Ligands and binding sites

AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 6 copies · chains A, B, C, D, E, F
2VJ · 2-[(2-{(1S,2S)-2-[(3,4-dichlorobenzyl)carbamoyl]cyclohexyl}-6-ethylpyrimidin-4-yl)sulfanyl]-1H-imidazole-5-carboxylic acid · ligand · 6 copies · chains A, C, B, D, E, F

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

Pockets

18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	814	0.84	0.86	95	AGS, 2VJ
2	549	0.78	0.84	57	AGS, 2VJ
3	535	0.77	0.84	53	AGS, 2VJ
4	283	0.77	0.89	43	empty
5	463	0.76	0.85	48	2VJ, AGS

Interfaces

13 interfaces between chains.

B–F · 1222 Å² buried · 12 hydrogen bonds · protein-protein
C–E · 1219 Å² buried · 13 hydrogen bonds · protein-protein
A–D · 1078 Å² buried · 16 hydrogen bonds · protein-protein
D–F · 611 Å² buried · 3 hydrogen bonds · protein-protein
E–F · 603 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

4NAH · Inhibitors of 4-Phosphopanthetheine Adenylyltransferase (PPAT) · the same entry in another collection · chain F against F, TM-score 1.00
P63820 · AlphaFold monomer V2.0 prediction for phosphopantetheine adenylyltransferase (P63820) · a predicted model of the same protein · chain C against A, TM-score 0.98

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 P63820
Elsewhere: RCSB PDB 4NAH · PDBe 4NAH · UniProt P63820

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