SMTL ID : 8tcz.1

Structure of PYCR1 complexed with 2-(pyridin-2-yl)cyclopropane-1-carboxylic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-10-mer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: V.253, 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 SO4.3: 7 residues within 4Å: Chain B: V.253, S.254, S.255, G.258, A.259, T.260 Ligands: ZRI.2 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.255, B:T.260 Water bridges: B:A.259, B:I.261 SO4.4: 5 residues within 4Å: Chain C: V.253, S.255, G.258, A.259, T.260 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:S.255, C:S.255, C:S.255, C:A.259, C:T.260, C:T.260 Water bridges: C:G.258 SO4.5: 3 residues within 4Å: Chain C: G.31, Q.32, L.33 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.32, C:L.33 SO4.6: 5 residues within 4Å: Chain D: V.253, S.255, G.258, A.259, T.260 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.255, D:T.260, D:T.260 Water bridges: D:G.258, D:A.259, D:A.259 SO4.7: 6 residues within 4Å: Chain E: V.253, S.254, 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:I.261 SO4.8: 5 residues within 4Å: Chain F: V.253, 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 SO4.10: 7 residues within 4Å: Chain G: V.253, S.254, S.255, G.258, A.259, T.260 Ligands: ZRI.9 5 PLIP interactions: 5 interactions with chain G Hydrogen bonds: G:S.255, G:T.260, G:T.260 Water bridges: G:A.259, G:I.261 SO4.11: 5 residues within 4Å: Chain H: V.253, S.255, G.258, A.259, T.260 7 PLIP interactions: 7 interactions with chain H Hydrogen bonds: H:S.255, H:S.255, H:S.255, H:A.259, H:T.260, H:T.260 Water bridges: H:G.258 SO4.12: 3 residues within 4Å: Chain H: G.31, Q.32, L.33 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:Q.32, H:L.33 SO4.13: 5 residues within 4Å: Chain I: V.253, S.255, G.258, A.259, T.260 7 PLIP interactions: 7 interactions with chain I Hydrogen bonds: I:S.255, I:T.260, I:T.260, I:T.260 Water bridges: I:G.258, I:A.259, I:A.259 SO4.14: 6 residues within 4Å: Chain J: V.253, S.254, S.255, G.258, A.259, T.260 6 PLIP interactions: 6 interactions with chain J Hydrogen bonds: J:S.255, J:S.255, J:S.255, J:A.259, J:T.260 Water bridges: J:I.261

2 x ZRI: (1S,2S)-2-(pyridin-2-yl)cyclopropane-1-carboxylic acid(Non-covalent)

ZRI.2: 12 residues within 4Å: Chain A: L.33, C.117, A.119, M.143, T.144, T.193 Chain B: V.253, S.255, G.258, A.259, T.260 Ligands: SO4.3 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:L.33, A:A.119, A:T.193, B:A.259 Hydrogen bonds: B:S.255, B:A.259, B:T.260 Water bridges: B:I.261 ZRI.9: 12 residues within 4Å: Chain F: L.33, C.117, A.119, M.143, T.144, T.193 Chain G: V.253, S.255, G.258, A.259, T.260 Ligands: SO4.10 9 PLIP interactions: 6 interactions with chain G, 3 interactions with chain F Hydrophobic interactions: G:A.259, F:L.33, F:A.119, F:T.193 Hydrogen bonds: G:S.255, G:A.259, G:T.260, G:T.260 Water bridges: G:I.261

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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