SMTL ID : 9s04.1

PYCR1 in complex with 1-(2,4-Difluorophenyl)-2-(1H-1,2,4-triazol-1- yl)ethanone

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.57 Å

Oligo State

homo-10-mer

Ligands

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

TLA.1: 11 residues within 4Å: Chain A: V.254, S.255, S.256, G.259, A.260, T.261 Chain B: K.94, A.119, A.120, L.291 Ligands: 01.5 9 PLIP interactions: 7 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 Water bridges: A:I.262 Salt bridges: B:K.94 TLA.4: 11 residues within 4Å: Chain A: K.94, A.119, A.120, L.291 Chain B: V.254, S.255, S.256, G.259, A.260, T.261 Ligands: 01.2 9 PLIP interactions: 2 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:A.120, B:S.256, B:S.256, B:S.256, B:S.256, B:A.260, B:T.261 Salt bridges: A:K.94 Water bridges: B:I.262 TLA.7: 11 residues within 4Å: Chain C: V.254, S.255, S.256, G.259, A.260, T.261 Chain D: K.94, A.119, A.120, L.291 Ligands: 01.11 9 PLIP interactions: 7 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:S.256, C:S.256, C:S.256, C:S.256, C:A.260, C:T.261, C:T.261, D:A.120 Salt bridges: D:K.94 TLA.10: 11 residues within 4Å: Chain C: K.94, A.119, A.120, S.199, L.291 Chain D: V.254, S.256, G.259, A.260, T.261 Ligands: 01.8 9 PLIP interactions: 7 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:S.256, D:S.256, D:S.256, D:A.260, D:T.261, C:A.120 Water bridges: D:T.261, D:T.261 Salt bridges: C:K.94 TLA.15: 10 residues within 4Å: Chain E: V.254, S.255, S.256, G.259, A.260, T.261 Chain J: K.94, A.120, L.291 Ligands: 01.32 10 PLIP interactions: 8 interactions with chain E, 2 interactions with chain J Hydrogen bonds: E:S.256, E:S.256, E:S.256, E:S.256, E:A.260, E:T.261, E:T.261, J:A.120 Water bridges: E:I.262 Salt bridges: J:K.94 TLA.17: 11 residues within 4Å: Chain F: V.254, S.255, S.256, G.259, A.260, T.261 Chain G: K.94, A.119, A.120, L.291 Ligands: 01.21 9 PLIP interactions: 7 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 Water bridges: F:I.262 Salt bridges: G:K.94 TLA.20: 11 residues within 4Å: Chain F: K.94, A.119, A.120, L.291 Chain G: V.254, S.255, S.256, G.259, A.260, T.261 Ligands: 01.18 9 PLIP interactions: 7 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 Water bridges: G:I.262 Salt bridges: F:K.94 TLA.23: 11 residues within 4Å: Chain H: V.254, S.255, S.256, G.259, A.260, T.261 Chain I: K.94, A.119, A.120, L.291 Ligands: 01.27 9 PLIP interactions: 7 interactions with chain H, 2 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:A.120 Salt bridges: I:K.94 TLA.26: 11 residues within 4Å: Chain H: K.94, A.119, A.120, S.199, L.291 Chain I: V.254, S.256, G.259, A.260, T.261 Ligands: 01.24 9 PLIP interactions: 7 interactions with chain I, 2 interactions with chain H Hydrogen bonds: I:S.256, I:S.256, I:S.256, I:A.260, I:T.261, H:A.120 Water bridges: I:T.261, I:T.261 Salt bridges: H:K.94 TLA.31: 10 residues within 4Å: Chain E: K.94, A.120, L.291 Chain J: V.254, S.255, S.256, G.259, A.260, T.261 Ligands: 01.16 10 PLIP interactions: 8 interactions with chain J, 2 interactions with chain E Hydrogen bonds: J:S.256, J:S.256, J:S.256, J:S.256, J:A.260, J:T.261, J:T.261, E:A.120 Water bridges: J:I.262 Salt bridges: E:K.94

10 x 01: 1-[2,4-bis(fluoranyl)phenyl]-2-(1,2,4-triazol-1-yl)ethanone

01.2: 11 residues within 4Å: Chain A: A.31, L.34, A.92, V.93, K.94, C.118, A.119, T.145, N.146, T.147 Ligands: TLA.4 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.34 Halogen bonds: A:C.118 01.5: 11 residues within 4Å: Chain B: A.31, L.34, A.92, V.93, K.94, C.118, A.119, T.145, N.146, T.147 Ligands: TLA.1 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.34 Halogen bonds: B:C.118 01.8: 11 residues within 4Å: Chain C: A.31, L.34, A.92, V.93, K.94, C.118, A.119, T.145, N.146, T.147 Ligands: TLA.10 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.34 Water bridges: C:A.31 Halogen bonds: C:C.118 01.11: 11 residues within 4Å: Chain D: A.31, L.34, A.92, V.93, K.94, C.118, A.119, T.145, N.146, T.147 Ligands: TLA.7 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.34 Halogen bonds: D:C.118 01.16: 11 residues within 4Å: Chain E: A.31, L.34, A.92, V.93, K.94, C.118, A.119, T.145, N.146, T.147 Ligands: TLA.31 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:L.34 Halogen bonds: E:C.118 01.18: 11 residues within 4Å: Chain F: A.31, L.34, A.92, V.93, K.94, C.118, A.119, T.145, N.146, T.147 Ligands: TLA.20 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:L.34 Halogen bonds: F:C.118 01.21: 11 residues within 4Å: Chain G: A.31, L.34, A.92, V.93, K.94, C.118, A.119, T.145, N.146, T.147 Ligands: TLA.17 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:L.34 Halogen bonds: G:C.118 01.24: 11 residues within 4Å: Chain H: A.31, L.34, A.92, V.93, K.94, C.118, A.119, T.145, N.146, T.147 Ligands: TLA.26 3 PLIP interactions: 3 interactions with chain H Hydrophobic interactions: H:L.34 Water bridges: H:A.31 Halogen bonds: H:C.118 01.27: 11 residues within 4Å: Chain I: A.31, L.34, A.92, V.93, K.94, C.118, A.119, T.145, N.146, T.147 Ligands: TLA.23 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:L.34 Halogen bonds: I:C.118 01.32: 11 residues within 4Å: Chain J: A.31, L.34, A.92, V.93, K.94, C.118, A.119, T.145, N.146, T.147 Ligands: TLA.15 2 PLIP interactions: 2 interactions with chain J Hydrophobic interactions: J:L.34 Halogen bonds: J:C.118

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

EDO.3: 5 residues within 4Å: Chain A: A.283, I.286, R.287, E.290 Chain B: H.263 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.283, A:R.287 Water bridges: A:R.287 EDO.6: 5 residues within 4Å: Chain A: H.263 Chain B: A.283, I.286, R.287, E.290 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.283, B:R.287 EDO.9: 6 residues within 4Å: Chain C: M.239, H.242, S.243, Q.245, L.250 Chain D: V.151 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:M.239, C:Q.245 Water bridges: C:N.253 EDO.12: 5 residues within 4Å: Chain C: V.150, V.151 Chain D: M.239, H.242, S.243 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:M.239 EDO.13: 5 residues within 4Å: Chain C: H.263 Chain D: A.283, I.286, R.287, E.290 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:A.283, D:R.287 EDO.14: 1 residues within 4Å: Chain D: M.24 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:M.24 EDO.19: 5 residues within 4Å: Chain F: A.283, I.286, R.287, E.290 Chain G: H.263 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:A.283, F:R.287 Water bridges: F:R.287 EDO.22: 5 residues within 4Å: Chain F: H.263 Chain G: A.283, I.286, R.287, E.290 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:A.283, G:R.287 EDO.25: 6 residues within 4Å: Chain H: M.239, H.242, S.243, Q.245, L.250 Chain I: V.151 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:M.239, H:Q.245 Water bridges: H:N.253 EDO.28: 5 residues within 4Å: Chain H: V.150, V.151 Chain I: M.239, H.242, S.243 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:M.239 EDO.29: 5 residues within 4Å: Chain H: H.263 Chain I: A.283, I.286, R.287, E.290 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:A.283, I:R.287 EDO.30: 1 residues within 4Å: Chain I: M.24 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:M.24

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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