SMTL ID : 8tcv.1

Structure of PYCR1 complexed with 4-bromobenzene-1,3-dicarboxylic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

homo-10-mer

Ligands

16 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 5 residues within 4Å: Chain A: V.253, S.255, G.258, A.259, T.260 Ligand excluded by PLIP SO4.2: 4 residues within 4Å: Chain A: H.241, S.242, E.243, Q.244 Ligand excluded by PLIP SO4.4: 4 residues within 4Å: Chain B: H.241, S.242, E.243, Q.244 Ligand excluded by PLIP SO4.5: 7 residues within 4Å: Chain B: V.253, S.254, S.255, G.258, A.259, T.260 Ligands: ZR0.3 Ligand excluded by PLIP SO4.6: 3 residues within 4Å: Chain C: G.31, Q.32, L.33 Ligand excluded by PLIP SO4.7: 5 residues within 4Å: Chain C: V.253, S.255, G.258, A.259, T.260 Ligand excluded by PLIP SO4.8: 6 residues within 4Å: Chain D: V.253, S.254, S.255, G.258, A.259, T.260 Ligand excluded by PLIP SO4.9: 5 residues within 4Å: Chain E: V.253, S.255, G.258, A.259, T.260 Ligand excluded by PLIP SO4.10: 5 residues within 4Å: Chain F: V.253, S.255, G.258, A.259, T.260 Ligand excluded by PLIP SO4.11: 4 residues within 4Å: Chain F: H.241, S.242, E.243, Q.244 Ligand excluded by PLIP SO4.13: 4 residues within 4Å: Chain G: H.241, S.242, E.243, Q.244 Ligand excluded by PLIP SO4.14: 7 residues within 4Å: Chain G: V.253, S.254, S.255, G.258, A.259, T.260 Ligands: ZR0.12 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain H: G.31, Q.32, L.33 Ligand excluded by PLIP SO4.16: 5 residues within 4Å: Chain H: V.253, S.255, G.258, A.259, T.260 Ligand excluded by PLIP SO4.17: 6 residues within 4Å: Chain I: V.253, S.254, S.255, G.258, A.259, T.260 Ligand excluded by PLIP SO4.18: 5 residues within 4Å: Chain J: V.253, S.255, G.258, A.259, T.260 Ligand excluded by PLIP

2 x ZR0: 4-bromobenzene-1,3-dicarboxylic acid(Non-covalent)

ZR0.3: 10 residues within 4Å: Chain A: A.119, M.143, T.144, G.197 Chain B: V.253, S.255, G.258, A.259, T.260 Ligands: SO4.5 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.255, B:A.259, B:T.260 Water bridges: B:I.261 Hydrophobic interactions: A:A.119 ZR0.12: 10 residues within 4Å: Chain F: A.119, M.143, T.144, G.197 Chain G: V.253, S.255, G.258, A.259, T.260 Ligands: SO4.14 6 PLIP interactions: 1 interactions with chain F, 5 interactions with chain G Hydrophobic interactions: F:A.119 Hydrogen bonds: G:S.255, G:A.259, G:T.260, G:T.260 Water bridges: G:I.261

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Meeks, K.R. et al., Novel Fragment Inhibitors of PYCR1 from Docking-Guided X-ray Crystallography. J.Chem.Inf.Model. (2024)

Release Date

2024-03-06

Peptides

Pyrroline-5-carboxylate reductase 1, mitochondrial: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
A

G
B

H
C

I
D

J
E

Pyrroline-5-carboxylate reductase 1, mitochondrial

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