SMTL ID : 8td1.1

Structure of PYCR1 complexed with 3-(6-Oxa-9-azaspiro(4.5)decane-9-carbonyl)benzoic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

homo-10-mer

Ligands

10 x ZRZ: 3-(6-oxa-9-azaspiro[4.5]decane-9-carbonyl)benzoic acid(Non-covalent)

ZRZ.1: 15 residues within 4Å: Chain A: N.252, V.253, G.258, A.259, T.260 Chain B: L.33, A.91, V.92, P.94, C.117, A.118, A.119, M.143, T.193 Ligands: SO4.4 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:A.119, B:T.193 Hydrogen bonds: B:A.119, A:A.259, A:T.260, A:T.260, A:T.260 ZRZ.2: 16 residues within 4Å: Chain A: Q.32, L.33, A.91, V.92, P.94, C.117, A.118, A.119, M.143, T.193 Chain B: N.252, V.253, S.255, G.258, A.259, T.260 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Q.32, A:A.119, A:T.193 Hydrogen bonds: A:A.119, B:A.259, B:T.260 ZRZ.5: 15 residues within 4Å: Chain C: N.252, V.253, 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 Ligands: SO4.8 8 PLIP interactions: 3 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:A.119, D:T.193 Hydrogen bonds: D:A.119, C:A.259, C:T.260, C:T.260, C:T.260 Water bridges: C:G.258 ZRZ.7: 14 residues within 4Å: Chain C: L.33, V.92, K.93, P.94, C.117, A.118, A.119, M.143, T.193 Chain D: V.253, 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 Hydrophobic interactions: C:A.119, C:T.193 ZRZ.9: 13 residues within 4Å: Chain E: V.253, S.255, G.258, A.259, T.260 Chain J: L.33, V.92, P.94, C.117, A.118, A.119, M.143 Ligands: SO4.20 8 PLIP interactions: 6 interactions with chain E, 2 interactions with chain J Hydrogen bonds: E:A.259, E:T.260, E:T.260, E:T.260, J:A.119 Water bridges: E:S.255, E:G.258 Hydrophobic interactions: J:A.119 ZRZ.11: 15 residues within 4Å: Chain F: N.252, V.253, G.258, A.259, T.260 Chain G: L.33, A.91, V.92, P.94, C.117, A.118, A.119, M.143, T.193 Ligands: SO4.14 6 PLIP interactions: 3 interactions with chain F, 3 interactions with chain G Hydrogen bonds: F:A.259, F:T.260, F:T.260, G:A.119 Hydrophobic interactions: G:A.119, G:T.193 ZRZ.12: 16 residues within 4Å: Chain F: Q.32, L.33, A.91, V.92, P.94, C.117, A.118, A.119, M.143, T.193 Chain G: N.252, V.253, S.255, G.258, A.259, T.260 7 PLIP interactions: 4 interactions with chain F, 3 interactions with chain G Hydrophobic interactions: F:Q.32, F:A.119, F:T.193 Hydrogen bonds: F:A.119, G:A.259, G:T.260, G:T.260 ZRZ.15: 15 residues within 4Å: Chain H: N.252, V.253, 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 Ligands: SO4.18 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:G.258 Hydrophobic interactions: I:A.119, I:T.193 ZRZ.17: 14 residues within 4Å: Chain H: L.33, V.92, K.93, P.94, C.117, A.118, A.119, M.143, T.193 Chain I: V.253, G.258, A.259, T.260 Ligands: SO4.16 8 PLIP interactions: 3 interactions with chain H, 5 interactions with chain I Hydrophobic interactions: H:A.119, H:T.193 Hydrogen bonds: H:A.119, I:A.259, I:T.260, I:T.260 Water bridges: I:S.255, I:S.255 ZRZ.19: 13 residues within 4Å: Chain E: L.33, V.92, P.94, C.117, A.118, A.119, M.143 Chain J: V.253, S.255, G.258, A.259, T.260 Ligands: SO4.10 7 PLIP interactions: 5 interactions with chain J, 2 interactions with chain E Hydrogen bonds: J:A.259, J:T.260, J:T.260, E:A.119 Water bridges: J:S.255, J:G.258 Hydrophobic interactions: E:A.119

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 4 residues within 4Å: Chain A: V.150, R.151 Chain B: K.237, H.241 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.237 PEG.13: 4 residues within 4Å: Chain F: V.150, R.151 Chain G: K.237, H.241 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:K.237

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

SO4.4: 4 residues within 4Å: Chain B: G.31, Q.32, K.93 Ligands: ZRZ.1 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.32 Water bridges: B:L.33 Salt bridges: B:K.93 SO4.6: 4 residues within 4Å: Chain C: G.31, Q.32, K.93 Ligands: ZRZ.7 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.32 Salt bridges: C:K.93 SO4.8: 4 residues within 4Å: Chain D: G.31, Q.32, K.93 Ligands: ZRZ.5 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.32 Water bridges: D:L.33 Salt bridges: D:K.93 SO4.10: 4 residues within 4Å: Chain E: G.31, Q.32, K.93 Ligands: ZRZ.19 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:Q.32 Water bridges: E:L.33, E:A.91 Salt bridges: E:K.93 SO4.14: 4 residues within 4Å: Chain G: G.31, Q.32, K.93 Ligands: ZRZ.11 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:Q.32 Water bridges: G:L.33 Salt bridges: G:K.93 SO4.16: 4 residues within 4Å: Chain H: G.31, Q.32, K.93 Ligands: ZRZ.17 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:Q.32 Salt bridges: H:K.93 SO4.18: 4 residues within 4Å: Chain I: G.31, Q.32, K.93 Ligands: ZRZ.15 3 PLIP interactions: 3 interactions with chain I Hydrogen bonds: I:Q.32 Water bridges: I:L.33 Salt bridges: I:K.93 SO4.20: 4 residues within 4Å: Chain J: G.31, Q.32, K.93 Ligands: ZRZ.9 4 PLIP interactions: 4 interactions with chain J Hydrogen bonds: J:Q.32 Water bridges: J:L.33, J:A.91 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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