SMTL ID : 9b2e.1

DHNA associated with an inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-octamer

Ligands

8 x B55: 2-amino-8-sulfanyl-1,9-dihydro-6H-purin-6-one(Non-covalent)

B55.1: 13 residues within 4Å: Chain A: I.5, L.48, T.51, Y.52, D.53, Y.54, V.55 Chain E: V.18, Y.19, L.72, I.73, E.74, V.113 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain E Hydrogen bonds: A:T.51, A:T.51, A:D.53, A:Y.54, E:I.73 pi-Stacking: A:Y.54, A:Y.54 Water bridges: E:V.18, E:V.18 Salt bridges: E:E.74 B55.2: 12 residues within 4Å: Chain B: I.5, L.48, T.51, Y.52, D.53, Y.54 Chain H: V.18, Y.19, L.72, I.73, E.74, V.113 9 PLIP interactions: 3 interactions with chain H, 6 interactions with chain B Hydrogen bonds: H:I.73, B:T.51, B:D.53, B:D.53, B:Y.54 Water bridges: H:V.18 Salt bridges: H:E.74 pi-Stacking: B:Y.54, B:Y.54 B55.3: 13 residues within 4Å: Chain C: I.5, L.48, T.51, Y.52, D.53, Y.54, V.55 Chain G: V.18, Y.19, L.72, I.73, E.74, V.113 10 PLIP interactions: 4 interactions with chain G, 6 interactions with chain C Hydrogen bonds: G:I.73, C:T.51, C:T.51, C:D.53, C:Y.54 Water bridges: G:V.18, G:V.18 Salt bridges: G:E.74 pi-Stacking: C:Y.54, C:Y.54 B55.4: 12 residues within 4Å: Chain D: I.5, L.48, T.51, Y.52, D.53, Y.54 Chain F: V.18, Y.19, L.72, I.73, E.74, V.113 9 PLIP interactions: 6 interactions with chain D, 3 interactions with chain F Hydrogen bonds: D:T.51, D:D.53, D:D.53, D:Y.54, F:I.73 pi-Stacking: D:Y.54, D:Y.54 Water bridges: F:V.18 Salt bridges: F:E.74 B55.5: 13 residues within 4Å: Chain C: V.18, Y.19, L.72, I.73, E.74, V.113 Chain E: I.5, L.48, T.51, Y.52, D.53, Y.54, V.55 10 PLIP interactions: 6 interactions with chain E, 4 interactions with chain C Hydrogen bonds: E:T.51, E:T.51, E:D.53, E:Y.54, C:I.73 pi-Stacking: E:Y.54, E:Y.54 Water bridges: C:V.18, C:V.18 Salt bridges: C:E.74 B55.6: 12 residues within 4Å: Chain B: V.18, Y.19, L.72, I.73, E.74, V.113 Chain F: I.5, L.48, T.51, Y.52, D.53, Y.54 9 PLIP interactions: 6 interactions with chain F, 3 interactions with chain B Hydrogen bonds: F:T.51, F:D.53, F:D.53, F:Y.54, B:I.73 pi-Stacking: F:Y.54, F:Y.54 Water bridges: B:V.18 Salt bridges: B:E.74 B55.7: 13 residues within 4Å: Chain A: V.18, Y.19, L.72, I.73, E.74, V.113 Chain G: I.5, L.48, T.51, Y.52, D.53, Y.54, V.55 10 PLIP interactions: 6 interactions with chain G, 4 interactions with chain A Hydrogen bonds: G:T.51, G:T.51, G:D.53, G:Y.54, A:I.73 pi-Stacking: G:Y.54, G:Y.54 Water bridges: A:V.18, A:V.18 Salt bridges: A:E.74 B55.8: 12 residues within 4Å: Chain D: V.18, Y.19, L.72, I.73, E.74, V.113 Chain H: I.5, L.48, T.51, Y.52, D.53, Y.54 9 PLIP interactions: 3 interactions with chain D, 6 interactions with chain H Hydrogen bonds: D:I.73, H:T.51, H:D.53, H:D.53, H:Y.54 Water bridges: D:V.18 Salt bridges: D:E.74 pi-Stacking: H:Y.54, H:Y.54

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Czeczot, A.M. et al., Crystal structure of dihydroneopterin aldolase from Mycobacterium tuberculosis associated with 8-mercaptoguanine, and development of novel S8-functionalized analogues as inhibitors: Synthesis, enzyme inhibition, in vitro toxicity and antitubercular activity. J Enzyme Inhib Med Chem (2024)

Release Date

2025-02-19

Peptides

7,8-dihydroneopterin aldolase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

7,8-dihydroneopterin aldolase