SMTL ID : 9rzz.1

PYCR1 in complex with pyrrolidine-1-sulfonic acid.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-10-mer

Ligands

20 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 4 residues within 4Å: Chain A: G.31, Q.32, L.33, K.93 Ligand excluded by PLIP EDO.3: 5 residues within 4Å: Chain A: R.288 Chain B: K.216, M.217 Chain C: R.286 Chain D: H.262 Ligand excluded by PLIP EDO.4: 4 residues within 4Å: Chain B: G.31, Q.32, L.33, K.93 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain B: H.262 Chain F: K.216, M.217 Chain G: R.288 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain C: S.269, G.270, G.271 Chain J: S.269, G.270, G.271 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain C: G.31, Q.32, L.33, K.93 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain C: H.262 Chain E: K.216, M.217 Chain J: R.288 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: S.269, G.270 Chain D: S.269, G.270, G.271 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain D: G.31, Q.32, L.33, K.93 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain E: G.31, Q.32, L.33, A.91, K.93 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain F: G.31, Q.32, L.33, K.93 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain F: R.288 Chain G: K.216, M.217 Chain H: R.286 Chain I: H.262 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain G: G.31, Q.32, L.33, K.93 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain A: K.216, M.217 Chain B: R.288 Chain G: H.262 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain E: S.269, G.270, G.271 Chain H: S.269, G.270, G.271 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain H: G.31, Q.32, L.33, K.93 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain E: R.288 Chain H: H.262 Chain J: K.216, M.217 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain F: S.269, G.270 Chain I: S.269, G.270, G.271 Ligand excluded by PLIP EDO.27: 4 residues within 4Å: Chain I: G.31, Q.32, L.33, K.93 Ligand excluded by PLIP EDO.29: 5 residues within 4Å: Chain J: G.31, Q.32, L.33, A.91, K.93 Ligand excluded by PLIP

10 x 01: pyrrolidine-1-sulfonic acid

01.2: 9 residues within 4Å: Chain A: V.253, S.255, G.258, A.259, T.260 Chain B: M.143, T.193, G.197, S.198 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.255, A:A.259, A:T.260, A:T.260 Water bridges: A:V.253, A:S.255, A:G.258 Hydrophobic interactions: B:T.193 01.6: 8 residues within 4Å: Chain A: T.193, G.197, S.198 Chain B: V.253, S.255, G.258, A.259, T.260 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.255, B:A.259, B:T.260 Water bridges: B:S.255, B:S.255, B:G.258, B:I.261 Hydrophobic interactions: A:T.193 01.9: 9 residues within 4Å: Chain C: V.253, S.255, G.258, A.259, T.260 Chain D: M.143, T.193, G.197, S.198 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:S.255, C:A.259, C:T.260, C:T.260 Water bridges: C:V.253, C:S.255, C:G.258, C:I.261 Hydrophobic interactions: D:T.193 01.13: 9 residues within 4Å: Chain C: M.143, T.193, G.197, S.198 Chain D: V.253, S.255, G.258, A.259, T.260 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.255, D:A.259, D:T.260 Water bridges: D:G.258, D:I.261 Hydrophobic interactions: C:T.193 01.15: 8 residues within 4Å: Chain E: V.253, S.255, G.258, A.259, T.260 Chain J: T.193, G.197, S.198 9 PLIP interactions: 8 interactions with chain E, 1 interactions with chain J Hydrogen bonds: E:S.255, E:A.259, E:T.260, E:T.260 Water bridges: E:S.255, E:S.255, E:G.258, E:I.261 Hydrophobic interactions: J:T.193 01.17: 9 residues within 4Å: Chain F: V.253, S.255, G.258, A.259, T.260 Chain G: M.143, T.193, G.197, S.198 8 PLIP interactions: 7 interactions with chain F, 1 interactions with chain G Hydrogen bonds: F:S.255, F:A.259, F:T.260, F:T.260 Water bridges: F:V.253, F:S.255, F:G.258 Hydrophobic interactions: G:T.193 01.21: 8 residues within 4Å: Chain F: T.193, G.197, S.198 Chain G: V.253, S.255, G.258, A.259, T.260 8 PLIP interactions: 7 interactions with chain G, 1 interactions with chain F Hydrogen bonds: G:S.255, G:A.259, G:T.260 Water bridges: G:S.255, G:S.255, G:G.258, G:I.261 Hydrophobic interactions: F:T.193 01.24: 9 residues within 4Å: Chain H: V.253, S.255, G.258, A.259, T.260 Chain I: M.143, T.193, G.197, S.198 9 PLIP interactions: 1 interactions with chain I, 8 interactions with chain H Hydrophobic interactions: I:T.193 Hydrogen bonds: H:S.255, H:A.259, H:T.260, H:T.260 Water bridges: H:V.253, H:S.255, H:G.258, H:I.261 01.28: 9 residues within 4Å: Chain H: M.143, T.193, G.197, S.198 Chain I: V.253, S.255, G.258, A.259, T.260 6 PLIP interactions: 5 interactions with chain I, 1 interactions with chain H Hydrogen bonds: I:S.255, I:A.259, I:T.260 Water bridges: I:G.258, I:I.261 Hydrophobic interactions: H:T.193 01.30: 8 residues within 4Å: Chain E: T.193, G.197, S.198 Chain J: V.253, S.255, G.258, A.259, T.260 9 PLIP interactions: 8 interactions with chain J, 1 interactions with chain E Hydrogen bonds: J:S.255, J:A.259, J:T.260, J:T.260 Water bridges: J:S.255, J:S.255, J:G.258, J:I.261 Hydrophobic interactions: E:T.193

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ragin-Oh, W. et al., Crystallographic fragment screening reveals new starting points for PYCR1 inhibitor design. Bioorg.Chem. (2025)

Release Date

2025-10-15

Peptides

Isoform 3 of 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

Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial