SMTL ID : 8td0.1

Structure of PYCR1 complexed with 5-oxo-7a-phenyl-hexahydropyrrolo[2,1-b][1,3]thiazole-3-carboxylic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-10-mer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: Q.32, L.61, A.62, T.63 Chain D: R.222 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:Q.32, A:A.62, A:T.63 Salt bridges: D:R.222 SO4.2: 6 residues within 4Å: Chain A: V.253, S.254, S.255, G.258, A.259, T.260 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.255, A:S.255, A:S.255, A:A.259, A:T.260, A:T.260 Water bridges: A:I.261 SO4.5: 5 residues within 4Å: Chain D: V.253, S.255, G.258, A.259, T.260 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:S.255, D:S.255, D:T.260, D:T.260, D:T.260 SO4.6: 5 residues within 4Å: Chain E: V.253, S.255, G.258, A.259, T.260 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:S.255, E:S.255, E:S.255, E:A.259, E:T.260, E:T.260 Water bridges: E:G.258 SO4.7: 5 residues within 4Å: Chain F: Q.32, L.61, A.62, T.63 Chain I: R.222 4 PLIP interactions: 1 interactions with chain I, 3 interactions with chain F Salt bridges: I:R.222 Hydrogen bonds: F:Q.32, F:A.62, F:T.63 SO4.8: 6 residues within 4Å: Chain F: V.253, S.254, S.255, G.258, A.259, T.260 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:S.255, F:S.255, F:S.255, F:A.259, F:T.260 Water bridges: F:I.261 SO4.11: 5 residues within 4Å: Chain I: V.253, S.255, G.258, A.259, T.260 5 PLIP interactions: 5 interactions with chain I Hydrogen bonds: I:S.255, I:S.255, I:T.260, I:T.260, I:T.260 SO4.12: 5 residues within 4Å: Chain J: V.253, S.255, G.258, A.259, T.260 7 PLIP interactions: 7 interactions with chain J Hydrogen bonds: J:S.255, J:S.255, J:S.255, J:A.259, J:T.260, J:T.260 Water bridges: J:G.258

4 x ZS5: (3R,4S,7aR)-5-oxo-7a-phenylhexahydropyrrolo[2,1-b][1,3]thiazole-3-carboxylic acid(Non-covalent)

ZS5.3: 12 residues within 4Å: Chain A: L.33, C.117, A.119, T.144, N.145, T.146, G.197 Chain B: N.252, V.253, S.255, A.259, T.260 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.33, A:L.33, A:L.33, A:T.146 Hydrogen bonds: A:A.119, B:S.255, B:A.259, B:T.260 Water bridges: B:G.258 ZS5.4: 11 residues within 4Å: Chain C: N.252, V.253, S.255, A.259, T.260 Chain D: Q.32, L.33, C.117, A.119, T.146, G.197 11 PLIP interactions: 5 interactions with chain D, 6 interactions with chain C Hydrophobic interactions: D:Q.32, D:L.33, D:L.33, D:T.146 Hydrogen bonds: D:A.119, C:S.255, C:A.259, C:T.260, C:T.260 Water bridges: C:S.255, C:S.255 ZS5.9: 12 residues within 4Å: Chain F: L.33, C.117, A.119, T.144, N.145, T.146, G.197 Chain G: N.252, V.253, S.255, A.259, T.260 10 PLIP interactions: 5 interactions with chain G, 5 interactions with chain F Hydrogen bonds: G:S.255, G:A.259, G:T.260, G:T.260, F:A.119 Water bridges: G:G.258 Hydrophobic interactions: F:L.33, F:L.33, F:L.33, F:T.146 ZS5.10: 11 residues within 4Å: Chain H: N.252, V.253, S.255, A.259, T.260 Chain I: Q.32, L.33, C.117, A.119, T.146, G.197 10 PLIP interactions: 5 interactions with chain I, 5 interactions with chain H Hydrophobic interactions: I:Q.32, I:L.33, I:L.33, I:T.146 Hydrogen bonds: I:A.119, H:S.255, H:A.259, H:T.260 Water bridges: H:S.255, H:S.255

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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