SMTL ID : 8tcu.1

Structure of PYCR1 complexed with 2-chloro-5-(2-oxoimidazolidin-1-yl)benzoic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-10-mer

Ligands

10 x ZR3: 2-chloro-5-(2-oxoimidazolidin-1-yl)benzoic acid(Non-covalent)

ZR3.1: 15 residues within 4Å: Chain A: G.258, A.259, T.260 Chain B: L.33, A.91, V.92, K.93, P.94, A.118, A.119, M.143, T.193, G.197, S.198 Ligands: SO4.4 10 PLIP interactions: 2 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:A.119, A:A.259, A:T.260, A:T.260, A:T.260 Halogen bonds: B:S.198 Water bridges: A:S.255, A:S.255, A:G.258, A:I.261 ZR3.3: 15 residues within 4Å: Chain A: L.33, A.91, V.92, P.94, C.117, A.118, A.119, M.143, T.193, G.197, S.198 Chain B: G.258, A.259, T.260 Ligands: SO4.2 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:A.259, B:T.260, A:A.119 Water bridges: B:G.258 Halogen bonds: A:S.198 ZR3.5: 15 residues within 4Å: Chain C: G.258, A.259, T.260 Chain D: L.33, A.91, V.92, P.94, C.117, A.118, A.119, M.143, T.193, G.197, S.198 Ligands: SO4.8 9 PLIP interactions: 2 interactions with chain D, 7 interactions with chain C Hydrogen bonds: D:A.119, C:A.259, C:T.260, C:T.260, C:T.260 Halogen bonds: D:S.198 Water bridges: C:S.255, C:S.255, C:G.258 ZR3.7: 13 residues within 4Å: Chain C: L.33, V.92, P.94, A.118, A.119, M.143, T.193, G.197, S.198 Chain D: G.258, A.259, T.260 Ligands: SO4.6 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:A.259, D:T.260, C:A.119 Water bridges: D:S.255, D:S.255 pi-Cation interactions: C:K.93 Halogen bonds: C:S.198 ZR3.9: 13 residues within 4Å: Chain E: G.258, A.259, T.260 Chain J: L.33, A.91, V.92, P.94, A.118, A.119, M.143, T.193, G.197, S.198 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 Halogen bonds: J:S.198 ZR3.11: 15 residues within 4Å: Chain F: G.258, A.259, T.260 Chain G: L.33, A.91, V.92, K.93, P.94, A.118, A.119, M.143, T.193, G.197, S.198 Ligands: SO4.14 9 PLIP interactions: 7 interactions with chain F, 2 interactions with chain G Hydrogen bonds: F:A.259, F:T.260, F:T.260, G:A.119 Water bridges: F:S.255, F:S.255, F:G.258, F:I.261 Halogen bonds: G:S.198 ZR3.13: 15 residues within 4Å: Chain F: L.33, A.91, V.92, P.94, C.117, A.118, A.119, M.143, T.193, G.197, S.198 Chain G: G.258, A.259, T.260 Ligands: SO4.12 6 PLIP interactions: 2 interactions with chain F, 4 interactions with chain G Hydrogen bonds: F:A.119, G:A.259, G:T.260, G:T.260 Halogen bonds: F:S.198 Water bridges: G:G.258 ZR3.15: 15 residues within 4Å: Chain H: G.258, A.259, T.260 Chain I: L.33, A.91, V.92, P.94, C.117, A.118, A.119, M.143, T.193, G.197, S.198 Ligands: SO4.18 8 PLIP interactions: 6 interactions with chain H, 2 interactions with chain I Hydrogen bonds: H:A.259, H:T.260, H:T.260, I:A.119 Water bridges: H:S.255, H:S.255, H:G.258 Halogen bonds: I:S.198 ZR3.17: 13 residues within 4Å: Chain H: L.33, V.92, P.94, A.118, A.119, M.143, T.193, G.197, S.198 Chain I: G.258, A.259, T.260 Ligands: SO4.16 8 PLIP interactions: 3 interactions with chain H, 5 interactions with chain I Hydrogen bonds: H:A.119, I:A.259, I:T.260, I:T.260 pi-Cation interactions: H:K.93 Halogen bonds: H:S.198 Water bridges: I:S.255, I:S.255 ZR3.19: 13 residues within 4Å: Chain E: L.33, A.91, V.92, P.94, A.118, A.119, M.143, T.193, G.197, S.198 Chain J: G.258, A.259, T.260 7 PLIP interactions: 4 interactions with chain J, 3 interactions with chain E Hydrogen bonds: J:A.259, J:T.260, J:T.260, E:A.119 Water bridges: J:G.258 Hydrophobic interactions: E:A.119 Halogen bonds: E:S.198

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

SO4.2: 5 residues within 4Å: Chain A: G.31, Q.32, L.33, K.93 Ligands: ZR3.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.32, A:L.33 Salt bridges: A:K.93 SO4.4: 5 residues within 4Å: Chain B: G.31, Q.32, L.33, K.93 Ligands: ZR3.1 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.32, B:L.33 Water bridges: B:G.31, B:G.31, B:A.34, B:K.93 Salt bridges: B:K.93 SO4.6: 5 residues within 4Å: Chain C: G.31, Q.32, L.33, K.93 Ligands: ZR3.7 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.32, C:L.33 Water bridges: C:A.34 Salt bridges: C:K.93 SO4.8: 6 residues within 4Å: Chain D: G.31, Q.32, L.33, A.91, K.93 Ligands: ZR3.5 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.32, D:L.33 Salt bridges: D:K.93 SO4.10: 4 residues within 4Å: Chain E: G.31, Q.32, L.33, K.93 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:Q.32, E:L.33 Water bridges: E:G.31, E:A.34 Salt bridges: E:K.93 SO4.12: 5 residues within 4Å: Chain F: G.31, Q.32, L.33, K.93 Ligands: ZR3.13 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:Q.32, F:L.33 Salt bridges: F:K.93 SO4.14: 5 residues within 4Å: Chain G: G.31, Q.32, L.33, K.93 Ligands: ZR3.11 7 PLIP interactions: 7 interactions with chain G Hydrogen bonds: G:Q.32, G:L.33 Water bridges: G:G.31, G:G.31, G:A.34, G:K.93 Salt bridges: G:K.93 SO4.16: 5 residues within 4Å: Chain H: G.31, Q.32, L.33, K.93 Ligands: ZR3.17 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:Q.32, H:L.33 Water bridges: H:A.34 Salt bridges: H:K.93 SO4.18: 6 residues within 4Å: Chain I: G.31, Q.32, L.33, A.91, K.93 Ligands: ZR3.15 3 PLIP interactions: 3 interactions with chain I Hydrogen bonds: I:Q.32, I:L.33 Salt bridges: I:K.93 SO4.20: 4 residues within 4Å: Chain J: G.31, Q.32, L.33, K.93 5 PLIP interactions: 5 interactions with chain J Hydrogen bonds: J:Q.32, J:L.33 Water bridges: J:G.31, 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

Related Entries With Identical Sequence