SMTL ID : 8dbb.1

Crystal structure of DDT with the selective inhibitor 2,5-Pyridinedicarboxylic Acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-trimer

Ligands

3 x R3K: pyridine-2,5-dicarboxylic acid(Non-covalent)

R3K.1: 8 residues within 4Å: Chain A: P.2, F.3, R.37, S.64, I.65, I.108, K.110, M.115 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.108 Hydrogen bonds: A:P.2, A:I.65 Water bridges: A:R.37, A:R.37 Salt bridges: A:K.33, A:R.37, A:K.110 R3K.3: 10 residues within 4Å: Chain B: P.2, F.3, K.33, R.37, N.39, S.64, I.65, I.108, K.110, M.115 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.3, B:I.108 Hydrogen bonds: B:P.2, B:N.39, B:N.39, B:I.65 Salt bridges: B:K.33, B:K.110 R3K.4: 10 residues within 4Å: Chain C: P.2, F.3, K.33, R.37, N.39, S.64, I.65, I.108, K.110, M.115 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:F.3, C:I.108 Hydrogen bonds: C:P.2, C:N.39, C:N.39, C:I.65 Water bridges: C:K.33, C:K.33, C:K.110, C:K.110, C:K.110 Salt bridges: C:K.33, C:K.110

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.2: 8 residues within 4Å: Chain A: R.37, M.115, L.118 Chain C: A.26, S.29, I.30, H.80, F.84 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain C Hydrogen bonds: A:L.118, C:S.29 Salt bridges: A:R.37, A:K.110, C:H.80 Hydrophobic interactions: C:A.26, C:I.30 Water bridges: C:A.26, C:A.26

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Parkins, A. et al., 2,5-Pyridinedicarboxylic acid is a bioactive and highly selective inhibitor of D-dopachrome tautomerase. Structure (2023)

Release Date

2023-03-08

Peptides

D-dopachrome decarboxylase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D-dopachrome decarboxylase