SMTL ID : 9s02.1

PYCR1 in complex with 3-(2-thiazolyl)propionic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-10-mer

Ligands

10 x R9M: 3-(1,3-thiazol-2-yl)propanoic acid(Non-covalent)

R9M.1: 12 residues within 4Å: Chain A: V.254, S.256, G.259, A.260, T.261 Chain B: L.34, C.118, M.144, T.145, G.198, L.291 Ligands: EDO.3 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.256, A:A.260, A:T.261 Water bridges: A:S.256, A:S.256, A:G.259, B:A.120 R9M.12: 10 residues within 4Å: Chain A: C.118, M.144, T.145, G.198, L.291 Chain B: S.256, G.259, A.260, T.261 Ligands: EDO.14 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:V.254, B:S.256, B:A.260, B:T.261 Water bridges: B:S.256, B:G.259, A:A.120 R9M.22: 11 residues within 4Å: Chain C: S.256, G.259, A.260, T.261 Chain D: L.34, C.118, M.144, T.145, G.198, L.291 Ligands: EDO.24 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:V.254, C:S.256, C:A.260, C:T.261, C:T.261 Water bridges: C:S.256, C:G.259, D:A.120 R9M.35: 11 residues within 4Å: Chain C: L.34, C.118, M.144, T.145, G.198, L.291 Chain D: S.256, G.259, A.260, T.261 Ligands: EDO.37 8 PLIP interactions: 1 interactions with chain C, 7 interactions with chain D Water bridges: C:A.120, D:S.256, D:G.259, D:I.262 Hydrogen bonds: D:V.254, D:S.256, D:A.260, D:T.261 R9M.43: 11 residues within 4Å: Chain E: S.256, G.259, A.260, T.261 Chain J: L.34, C.118, M.144, T.145, G.198, L.291 Ligands: EDO.45 7 PLIP interactions: 1 interactions with chain J, 6 interactions with chain E Water bridges: J:A.120, E:S.256 Hydrogen bonds: E:V.254, E:S.256, E:A.260, E:T.261, E:T.261 R9M.49: 12 residues within 4Å: Chain F: V.254, S.256, G.259, A.260, T.261 Chain G: L.34, C.118, M.144, T.145, G.198, L.291 Ligands: EDO.51 7 PLIP interactions: 6 interactions with chain F, 1 interactions with chain G Hydrogen bonds: F:S.256, F:A.260, F:T.261 Water bridges: F:S.256, F:S.256, F:G.259, G:A.120 R9M.60: 10 residues within 4Å: Chain F: C.118, M.144, T.145, G.198, L.291 Chain G: S.256, G.259, A.260, T.261 Ligands: EDO.62 7 PLIP interactions: 6 interactions with chain G, 1 interactions with chain F Hydrogen bonds: G:V.254, G:S.256, G:A.260, G:T.261 Water bridges: G:S.256, G:G.259, F:A.120 R9M.70: 11 residues within 4Å: Chain H: S.256, G.259, A.260, T.261 Chain I: L.34, C.118, M.144, T.145, G.198, L.291 Ligands: EDO.72 8 PLIP interactions: 7 interactions with chain H, 1 interactions with chain I Hydrogen bonds: H:V.254, H:S.256, H:A.260, H:T.261, H:T.261 Water bridges: H:S.256, H:G.259, I:A.120 R9M.83: 11 residues within 4Å: Chain H: L.34, C.118, M.144, T.145, G.198, L.291 Chain I: S.256, G.259, A.260, T.261 Ligands: EDO.85 8 PLIP interactions: 7 interactions with chain I, 1 interactions with chain H Hydrogen bonds: I:V.254, I:S.256, I:A.260, I:T.261 Water bridges: I:S.256, I:G.259, I:I.262, H:A.120 R9M.91: 11 residues within 4Å: Chain E: L.34, C.118, M.144, T.145, G.198, L.291 Chain J: S.256, G.259, A.260, T.261 Ligands: EDO.93 7 PLIP interactions: 6 interactions with chain J, 1 interactions with chain E Hydrogen bonds: J:V.254, J:S.256, J:A.260, J:T.261, J:T.261 Water bridges: J:S.256, E:A.120

76 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 6 residues within 4Å: Chain A: Q.33, F.36, A.37, T.147, V.150 Chain B: N.253 Ligand excluded by PLIP EDO.3: 6 residues within 4Å: Chain A: N.253, V.254 Chain B: Q.33, T.147 Ligands: R9M.1, DMS.5 Ligand excluded by PLIP EDO.4: 3 residues within 4Å: Chain A: D.188, D.191, R.289 Ligand excluded by PLIP EDO.6: 3 residues within 4Å: Chain A: N.279 Chain B: V.267, S.270 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: D.87, R.112, I.114, L.171 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: K.217, M.218, G.219 Chain B: R.289 Chain F: R.287 Chain G: G.258 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: P.257, G.258, G.259 Chain B: R.287, L.291 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: Q.249, D.252, N.253 Chain C: R.222 Ligands: DMS.5 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: E.153, G.180, F.181 Chain B: R.227, Q.231 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain A: N.253 Chain B: Q.33, F.36, A.37, T.147, V.150 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain A: Q.33, T.147 Chain B: N.253, V.254 Ligands: R9M.12, DMS.16 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain A: K.238 Chain B: K.40, A.44, V.150, V.151, R.152 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain A: R.227, Q.231 Chain B: R.152, E.153, G.180, F.181 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain B: F.21, Q.22, S.23, V.47 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain B: E.81, Q.84, H.85 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain A: E.153, K.238 Chain B: E.153, K.238 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain B: Q.249, D.252, N.253 Chain F: R.222 Ligands: DMS.16 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain C: Q.33, F.36, A.37, V.150 Chain D: N.253 Ligand excluded by PLIP EDO.24: 7 residues within 4Å: Chain C: N.253, V.254 Chain D: Q.33, L.34, T.147 Ligands: R9M.22, DMS.25 Ligand excluded by PLIP EDO.27: 3 residues within 4Å: Chain C: N.279 Chain D: V.267, S.270 Ligand excluded by PLIP EDO.28: 4 residues within 4Å: Chain C: Q.249, D.252, N.253 Ligands: DMS.25 Ligand excluded by PLIP EDO.29: 5 residues within 4Å: Chain C: P.257, G.258, G.259 Chain D: R.287, L.291 Ligand excluded by PLIP EDO.30: 6 residues within 4Å: Chain C: R.227, Q.231 Chain D: E.153, G.180, F.181 Ligands: DMS.40 Ligand excluded by PLIP EDO.31: 5 residues within 4Å: Chain C: D.87, R.112, I.114, R.139, L.171 Ligand excluded by PLIP EDO.32: 3 residues within 4Å: Chain C: T.160, G.161, T.162 Ligand excluded by PLIP EDO.33: 3 residues within 4Å: Chain C: G.32, Q.33, K.94 Ligand excluded by PLIP EDO.34: 3 residues within 4Å: Chain C: D.188, D.191, R.289 Ligand excluded by PLIP EDO.36: 6 residues within 4Å: Chain C: N.253 Chain D: Q.33, F.36, A.37, T.147, V.150 Ligand excluded by PLIP EDO.37: 5 residues within 4Å: Chain C: Q.33, T.147 Chain D: N.253, V.254 Ligands: R9M.35 Ligand excluded by PLIP EDO.38: 7 residues within 4Å: Chain A: R.274 Chain B: D.209, D.213 Chain C: D.209 Chain D: G.248, K.251, R.274 Ligand excluded by PLIP EDO.39: 6 residues within 4Å: Chain A: S.270 Chain D: G.271, G.272, S.275, L.276, N.279 Ligand excluded by PLIP EDO.41: 4 residues within 4Å: Chain B: R.222 Chain D: Q.249, D.252, N.253 Ligand excluded by PLIP EDO.42: 4 residues within 4Å: Chain C: K.238, H.242 Chain D: V.151, R.152 Ligand excluded by PLIP EDO.44: 5 residues within 4Å: Chain E: Q.33, F.36, A.37, T.147, V.150 Ligand excluded by PLIP EDO.45: 6 residues within 4Å: Chain E: N.253, V.254 Chain J: Q.33, L.34, T.147 Ligands: R9M.43 Ligand excluded by PLIP EDO.46: 3 residues within 4Å: Chain E: S.270, G.271 Chain J: L.276 Ligand excluded by PLIP EDO.47: 4 residues within 4Å: Chain E: E.153, G.180, F.181 Chain J: Q.231 Ligand excluded by PLIP EDO.48: 5 residues within 4Å: Chain E: A.44, V.150, V.151, R.152 Chain J: K.238 Ligand excluded by PLIP EDO.50: 6 residues within 4Å: Chain F: Q.33, F.36, A.37, T.147, V.150 Chain G: N.253 Ligand excluded by PLIP EDO.51: 6 residues within 4Å: Chain F: N.253, V.254 Chain G: Q.33, T.147 Ligands: R9M.49, DMS.53 Ligand excluded by PLIP EDO.52: 3 residues within 4Å: Chain F: D.188, D.191, R.289 Ligand excluded by PLIP EDO.54: 3 residues within 4Å: Chain F: N.279 Chain G: V.267, S.270 Ligand excluded by PLIP EDO.55: 4 residues within 4Å: Chain F: D.87, R.112, I.114, L.171 Ligand excluded by PLIP EDO.56: 6 residues within 4Å: Chain A: R.287 Chain B: G.258 Chain F: K.217, M.218, G.219 Chain G: R.289 Ligand excluded by PLIP EDO.57: 5 residues within 4Å: Chain F: P.257, G.258, G.259 Chain G: R.287, L.291 Ligand excluded by PLIP EDO.58: 5 residues within 4Å: Chain F: Q.249, D.252, N.253 Chain H: R.222 Ligands: DMS.53 Ligand excluded by PLIP EDO.59: 5 residues within 4Å: Chain F: E.153, G.180, F.181 Chain G: R.227, Q.231 Ligand excluded by PLIP EDO.61: 6 residues within 4Å: Chain F: N.253 Chain G: Q.33, F.36, A.37, T.147, V.150 Ligand excluded by PLIP EDO.62: 6 residues within 4Å: Chain F: Q.33, T.147 Chain G: N.253, V.254 Ligands: R9M.60, DMS.64 Ligand excluded by PLIP EDO.63: 6 residues within 4Å: Chain F: K.238 Chain G: K.40, A.44, V.150, V.151, R.152 Ligand excluded by PLIP EDO.65: 6 residues within 4Å: Chain F: R.227, Q.231 Chain G: R.152, E.153, G.180, F.181 Ligand excluded by PLIP EDO.66: 4 residues within 4Å: Chain G: F.21, Q.22, S.23, V.47 Ligand excluded by PLIP EDO.67: 3 residues within 4Å: Chain G: E.81, Q.84, H.85 Ligand excluded by PLIP EDO.68: 4 residues within 4Å: Chain F: E.153, K.238 Chain G: E.153, K.238 Ligand excluded by PLIP EDO.69: 5 residues within 4Å: Chain A: R.222 Chain G: Q.249, D.252, N.253 Ligands: DMS.64 Ligand excluded by PLIP EDO.71: 5 residues within 4Å: Chain H: Q.33, F.36, A.37, V.150 Chain I: N.253 Ligand excluded by PLIP EDO.72: 7 residues within 4Å: Chain H: N.253, V.254 Chain I: Q.33, L.34, T.147 Ligands: R9M.70, DMS.73 Ligand excluded by PLIP EDO.75: 3 residues within 4Å: Chain H: N.279 Chain I: V.267, S.270 Ligand excluded by PLIP EDO.76: 4 residues within 4Å: Chain H: Q.249, D.252, N.253 Ligands: DMS.73 Ligand excluded by PLIP EDO.77: 5 residues within 4Å: Chain H: P.257, G.258, G.259 Chain I: R.287, L.291 Ligand excluded by PLIP EDO.78: 6 residues within 4Å: Chain H: R.227, Q.231 Chain I: E.153, G.180, F.181 Ligands: DMS.88 Ligand excluded by PLIP EDO.79: 5 residues within 4Å: Chain H: D.87, R.112, I.114, R.139, L.171 Ligand excluded by PLIP EDO.80: 3 residues within 4Å: Chain H: T.160, G.161, T.162 Ligand excluded by PLIP EDO.81: 3 residues within 4Å: Chain H: G.32, Q.33, K.94 Ligand excluded by PLIP EDO.82: 3 residues within 4Å: Chain H: D.188, D.191, R.289 Ligand excluded by PLIP EDO.84: 6 residues within 4Å: Chain H: N.253 Chain I: Q.33, F.36, A.37, T.147, V.150 Ligand excluded by PLIP EDO.85: 5 residues within 4Å: Chain H: Q.33, T.147 Chain I: N.253, V.254 Ligands: R9M.83 Ligand excluded by PLIP EDO.86: 7 residues within 4Å: Chain F: R.274 Chain G: D.209, D.213 Chain H: D.209 Chain I: G.248, K.251, R.274 Ligand excluded by PLIP EDO.87: 6 residues within 4Å: Chain F: S.270 Chain I: G.271, G.272, S.275, L.276, N.279 Ligand excluded by PLIP EDO.89: 4 residues within 4Å: Chain G: R.222 Chain I: Q.249, D.252, N.253 Ligand excluded by PLIP EDO.90: 4 residues within 4Å: Chain H: K.238, H.242 Chain I: V.151, R.152 Ligand excluded by PLIP EDO.92: 5 residues within 4Å: Chain J: Q.33, F.36, A.37, T.147, V.150 Ligand excluded by PLIP EDO.93: 6 residues within 4Å: Chain E: Q.33, L.34, T.147 Chain J: N.253, V.254 Ligands: R9M.91 Ligand excluded by PLIP EDO.94: 3 residues within 4Å: Chain E: L.276 Chain J: S.270, G.271 Ligand excluded by PLIP EDO.95: 4 residues within 4Å: Chain E: Q.231 Chain J: E.153, G.180, F.181 Ligand excluded by PLIP EDO.96: 5 residues within 4Å: Chain E: K.238 Chain J: A.44, V.150, V.151, R.152 Ligand excluded by PLIP

10 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.5: 9 residues within 4Å: Chain A: D.252, N.253, S.255, S.256, P.257 Chain B: Q.33, K.94 Ligands: EDO.3, EDO.10 No protein-ligand interaction detected (PLIP) DMS.16: 8 residues within 4Å: Chain A: K.94 Chain B: D.252, N.253, S.255, S.256, P.257 Ligands: EDO.14, EDO.21 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.94 DMS.25: 9 residues within 4Å: Chain C: D.252, N.253, S.255, S.256, P.257 Chain D: Q.33, K.94 Ligands: EDO.24, EDO.28 No protein-ligand interaction detected (PLIP) DMS.26: 3 residues within 4Å: Chain C: R.223, L.224 Chain D: F.181 No protein-ligand interaction detected (PLIP) DMS.40: 5 residues within 4Å: Chain D: R.152, S.177, S.178, G.180 Ligands: EDO.30 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:E.153 DMS.53: 9 residues within 4Å: Chain F: D.252, N.253, S.255, S.256, P.257 Chain G: Q.33, K.94 Ligands: EDO.51, EDO.58 No protein-ligand interaction detected (PLIP) DMS.64: 8 residues within 4Å: Chain F: K.94 Chain G: D.252, N.253, S.255, S.256, P.257 Ligands: EDO.62, EDO.69 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:K.94 DMS.73: 9 residues within 4Å: Chain H: D.252, N.253, S.255, S.256, P.257 Chain I: Q.33, K.94 Ligands: EDO.72, EDO.76 No protein-ligand interaction detected (PLIP) DMS.74: 3 residues within 4Å: Chain H: R.223, L.224 Chain I: F.181 No protein-ligand interaction detected (PLIP) DMS.88: 5 residues within 4Å: Chain I: R.152, S.177, S.178, G.180 Ligands: EDO.78 1 PLIP interactions: 1 interactions with chain I Salt bridges: I:E.153

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ragin-Oh, W. et al., Crystallographic fragment screening reveals new starting points for PYCR1 inhibitor design. Bioorg.Chem. (2025)

Release Date

2025-10-15

Peptides

Isoform 3 of 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

Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial

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