SMTL ID : 9s01.1

PYCR1 in complex with L-tartrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-10-mer

Ligands

6 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.1: 10 residues within 4Å: Chain A: V.254, S.255, S.256, G.259, A.260, T.261 Chain B: K.94, A.120, S.199, L.291 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.256, A:S.256, A:S.256, A:S.256, A:A.260, A:T.261, B:A.120 Salt bridges: B:K.94 TLA.4: 9 residues within 4Å: Chain A: P.95, A.120, S.199, L.291 Chain B: V.254, S.256, G.259, A.260, T.261 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.256, B:S.256, B:S.256, B:S.256, B:A.260, B:T.261, A:A.120 Salt bridges: A:K.94 TLA.5: 9 residues within 4Å: Chain C: V.254, S.256, G.259, A.260, T.261 Chain D: P.95, A.120, S.199, L.291 10 PLIP interactions: 3 interactions with chain D, 7 interactions with chain C Hydrogen bonds: D:K.94, D:A.120, C:S.256, C:S.256, C:S.256, C:S.256, C:A.260, C:T.261, C:T.261 Salt bridges: D:K.94 TLA.8: 10 residues within 4Å: Chain F: V.254, S.255, S.256, G.259, A.260, T.261 Chain G: K.94, A.120, S.199, L.291 8 PLIP interactions: 6 interactions with chain F, 2 interactions with chain G Hydrogen bonds: F:S.256, F:S.256, F:S.256, F:S.256, F:A.260, F:T.261, G:A.120 Salt bridges: G:K.94 TLA.11: 9 residues within 4Å: Chain F: P.95, A.120, S.199, L.291 Chain G: V.254, S.256, G.259, A.260, T.261 8 PLIP interactions: 6 interactions with chain G, 2 interactions with chain F Hydrogen bonds: G:S.256, G:S.256, G:S.256, G:S.256, G:A.260, G:T.261, F:A.120 Salt bridges: F:K.94 TLA.12: 9 residues within 4Å: Chain H: V.254, S.256, G.259, A.260, T.261 Chain I: P.95, A.120, S.199, L.291 10 PLIP interactions: 7 interactions with chain H, 3 interactions with chain I Hydrogen bonds: H:S.256, H:S.256, H:S.256, H:S.256, H:A.260, H:T.261, H:T.261, I:K.94, I:A.120 Salt bridges: I:K.94

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

EDO.2: 5 residues within 4Å: Chain A: H.263 Chain B: R.287 Chain C: K.217, M.218 Chain D: R.289 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: A:H.263, B:R.287, C:M.218, D:R.289 EDO.3: 5 residues within 4Å: Chain A: K.217, M.218 Chain B: R.289 Chain F: R.287 Chain G: H.263 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 1 interactions with chain G Hydrogen bonds: B:R.289, B:R.289, A:M.218, G:H.263 EDO.6: 5 residues within 4Å: Chain C: R.289 Chain D: K.217, M.218 Chain E: R.287 Chain J: H.263 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 1 interactions with chain J Hydrogen bonds: C:R.289, D:M.218, J:H.263 EDO.7: 4 residues within 4Å: Chain A: R.289 Chain B: K.217, M.218 Chain D: H.263 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:R.289, A:R.289, D:H.263 Water bridges: A:E.282 EDO.9: 5 residues within 4Å: Chain F: H.263 Chain G: R.287 Chain H: K.217, M.218 Chain I: R.289 4 PLIP interactions: 1 interactions with chain G, 1 interactions with chain H, 1 interactions with chain I, 1 interactions with chain F Hydrogen bonds: G:R.287, H:M.218, I:R.289, F:H.263 EDO.10: 5 residues within 4Å: Chain A: R.287 Chain B: H.263 Chain F: K.217, M.218 Chain G: R.289 4 PLIP interactions: 1 interactions with chain F, 1 interactions with chain B, 2 interactions with chain G Hydrogen bonds: F:M.218, B:H.263, G:R.289, G:R.289 EDO.13: 5 residues within 4Å: Chain E: H.263 Chain H: R.289 Chain I: K.217, M.218 Chain J: R.287 3 PLIP interactions: 1 interactions with chain H, 1 interactions with chain E, 1 interactions with chain I Hydrogen bonds: H:R.289, E:H.263, I:M.218 EDO.14: 4 residues within 4Å: Chain F: R.289 Chain G: K.217, M.218 Chain I: H.263 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain I Hydrogen bonds: F:R.289, F:R.289, I:H.263 Water bridges: F:E.282

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

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