SMTL ID : 8tcw.1

Structure of PYCR1 complexed with 2-methyl-3-(2-oxoimidazolidin-1-yl)benzoic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

homo-10-mer

Ligands

10 x ZR6: 2-methyl-3-(2-oxoimidazolidin-1-yl)benzoic acid(Non-covalent)

ZR6.1: 12 residues within 4Å: Chain A: A.91, V.92, K.93, P.94, A.118, A.119, M.143 Chain B: S.255, G.258, A.259, T.260 Ligands: SO4.3 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:A.259, B:T.260, A:V.92, A:A.119 Hydrophobic interactions: A:A.119 pi-Cation interactions: A:K.93 ZR6.2: 11 residues within 4Å: Chain A: S.255, G.258, A.259, T.260 Chain B: V.92, P.94, C.117, A.118, A.119, M.143 Ligands: SO4.5 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:A.259, A:T.260, A:T.260, A:T.260, B:A.119 Water bridges: A:S.255 Hydrophobic interactions: B:A.119 pi-Cation interactions: B:K.93 ZR6.6: 11 residues within 4Å: Chain C: S.255, G.258, A.259, T.260 Chain D: V.92, P.94, C.117, A.118, A.119, M.143 Ligands: SO4.9 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:A.259, C:T.260, C:T.260, C:T.260, D:A.119 Water bridges: C:S.255 Hydrophobic interactions: D:A.119 pi-Cation interactions: D:K.93 ZR6.8: 12 residues within 4Å: Chain C: L.33, V.92, K.93, P.94, A.118, A.119, M.143 Chain D: S.255, G.258, A.259, T.260 Ligands: SO4.7 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:A.259, D:T.260, C:V.92, C:A.119 Water bridges: D:S.255 Hydrophobic interactions: C:A.119 pi-Cation interactions: C:K.93 ZR6.10: 10 residues within 4Å: Chain E: S.255, G.258, A.259, T.260 Chain J: V.92, P.94, A.118, A.119, M.143 Ligands: SO4.22 8 PLIP interactions: 5 interactions with chain E, 3 interactions with chain J Hydrogen bonds: E:A.259, E:T.260, E:T.260, E:T.260, J:A.119 Water bridges: E:G.258 Hydrophobic interactions: J:A.119 pi-Cation interactions: J:K.93 ZR6.12: 12 residues within 4Å: Chain F: A.91, V.92, K.93, P.94, A.118, A.119, M.143 Chain G: S.255, G.258, A.259, T.260 Ligands: SO4.14 7 PLIP interactions: 4 interactions with chain F, 3 interactions with chain G Hydrophobic interactions: F:A.119 Hydrogen bonds: F:V.92, F:A.119, G:A.259, G:T.260, G:T.260 pi-Cation interactions: F:K.93 ZR6.13: 11 residues within 4Å: Chain F: S.255, G.258, A.259, T.260 Chain G: V.92, P.94, C.117, A.118, A.119, M.143 Ligands: SO4.16 7 PLIP interactions: 4 interactions with chain F, 3 interactions with chain G Hydrogen bonds: F:A.259, F:T.260, F:T.260, G:A.119 Water bridges: F:S.255 Hydrophobic interactions: G:A.119 pi-Cation interactions: G:K.93 ZR6.17: 11 residues within 4Å: Chain H: S.255, G.258, A.259, T.260 Chain I: V.92, P.94, C.117, A.118, A.119, M.143 Ligands: SO4.20 7 PLIP interactions: 4 interactions with chain H, 3 interactions with chain I Hydrogen bonds: H:A.259, H:T.260, H:T.260, I:A.119 Water bridges: H:S.255 Hydrophobic interactions: I:A.119 pi-Cation interactions: I:K.93 ZR6.19: 12 residues within 4Å: Chain H: L.33, V.92, K.93, P.94, A.118, A.119, M.143 Chain I: S.255, G.258, A.259, T.260 Ligands: SO4.18 8 PLIP interactions: 4 interactions with chain H, 4 interactions with chain I Hydrophobic interactions: H:A.119 Hydrogen bonds: H:V.92, H:A.119, I:A.259, I:T.260, I:T.260 pi-Cation interactions: H:K.93 Water bridges: I:S.255 ZR6.21: 10 residues within 4Å: Chain E: V.92, P.94, A.118, A.119, M.143 Chain J: S.255, G.258, A.259, T.260 Ligands: SO4.11 8 PLIP interactions: 3 interactions with chain E, 5 interactions with chain J Hydrophobic interactions: E:A.119 Hydrogen bonds: E:A.119, J:A.259, J:T.260, J:T.260 pi-Cation interactions: E:K.93 Water bridges: J:G.258, J:T.260

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

SO4.3: 5 residues within 4Å: Chain A: G.31, Q.32, L.33, K.93 Ligands: ZR6.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.32, A:L.33 Water bridges: A:G.31, A:G.31, A:A.34 Salt bridges: A:K.93 SO4.4: 5 residues within 4Å: Chain A: Q.32, L.61, A.62, T.63 Chain D: R.222 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain A Salt bridges: D:R.222 Hydrogen bonds: A:Q.32, A:A.62, A:T.63 Water bridges: A:T.63 SO4.5: 5 residues within 4Å: Chain B: G.31, Q.32, L.33, K.93 Ligands: ZR6.2 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.32, B:L.33 Water bridges: B:A.34 Salt bridges: B:K.93 SO4.7: 5 residues within 4Å: Chain C: G.31, Q.32, L.33, K.93 Ligands: ZR6.8 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.32, C:L.33 Water bridges: C:G.31, C:K.93 Salt bridges: C:K.93 SO4.9: 5 residues within 4Å: Chain D: G.31, Q.32, L.33, K.93 Ligands: ZR6.6 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Q.32, D:L.33 Water bridges: D:G.31, D:G.31 Salt bridges: D:K.93 SO4.11: 5 residues within 4Å: Chain E: G.31, Q.32, L.33, K.93 Ligands: ZR6.21 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:Q.32, E:L.33 Water bridges: E:A.34 Salt bridges: E:K.93 SO4.14: 5 residues within 4Å: Chain F: G.31, Q.32, L.33, K.93 Ligands: ZR6.12 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:Q.32, F:L.33 Water bridges: F:G.31, F:G.31, F:A.34 Salt bridges: F:K.93 SO4.15: 5 residues within 4Å: Chain F: Q.32, L.61, A.62, T.63 Chain I: R.222 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain I Hydrogen bonds: F:Q.32, F:A.62, F:T.63 Salt bridges: I:R.222 SO4.16: 5 residues within 4Å: Chain G: G.31, Q.32, L.33, K.93 Ligands: ZR6.13 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:Q.32, G:L.33 Water bridges: G:A.34 Salt bridges: G:K.93 SO4.18: 5 residues within 4Å: Chain H: G.31, Q.32, L.33, K.93 Ligands: ZR6.19 5 PLIP interactions: 5 interactions with chain H Hydrogen bonds: H:Q.32, H:L.33 Water bridges: H:G.31, H:K.93 Salt bridges: H:K.93 SO4.20: 5 residues within 4Å: Chain I: G.31, Q.32, L.33, K.93 Ligands: ZR6.17 5 PLIP interactions: 5 interactions with chain I Hydrogen bonds: I:Q.32, I:L.33 Water bridges: I:G.31, I:G.31 Salt bridges: I:K.93 SO4.22: 5 residues within 4Å: Chain J: G.31, Q.32, L.33, K.93 Ligands: ZR6.10 4 PLIP interactions: 4 interactions with chain J Hydrogen bonds: J:Q.32, J:L.33 Water bridges: J:A.34 Salt bridges: J:K.93

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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