SMTL ID : 4fzj.2 (1 other biounit)

Pantothenate synthetase in complex with 1,3-DIMETHYL-1H-THIENO[2,3-C]PYRAZOLE-5-CARBOXYLIC ACID

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.63 Å

Oligo State

homo-dimer

Ligands

7 x EOH: ETHANOL(Non-functional Binders)

EOH.1: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.112 EOH.2: 5 residues within 4Å: Chain A: A.215, T.218 Chain B: H.222, T.225 Ligands: 0W1.5 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.225 EOH.3: 1 residues within 4Å: Chain A: N.176 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.176 EOH.15: 2 residues within 4Å: Chain B: R.236, L.250 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.236, B:R.236 EOH.16: 3 residues within 4Å: Chain B: S.15, A.16, A.108 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.16 EOH.17: 3 residues within 4Å: Chain B: D.254, I.255, G.256 1 PLIP interactions: 1 interactions with chain B Water bridges: B:I.255 EOH.18: 5 residues within 4Å: Chain B: L.147, Q.148, L.177, D.178, V.179 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.177 Hydrogen bonds: B:D.178, B:D.178, B:V.179 Water bridges: B:D.178

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

EDO.4: 7 residues within 4Å: Chain A: M.109, Y.110, G.113, L.114, R.115, T.116, K.145 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.109, A:R.115, A:K.145 EDO.6: 6 residues within 4Å: Chain A: H.44, G.46, H.47, L.50, G.158 Ligands: EDO.9 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.46, A:G.158 Water bridges: A:H.44, A:K.160, A:K.160 EDO.7: 5 residues within 4Å: Chain A: P.38, T.39, M.40, Q.72, V.142 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:P.38, A:Q.72, A:Q.72 Water bridges: A:M.40, A:Q.164 EDO.9: 9 residues within 4Å: Chain A: G.46, G.158, E.159, K.160, V.184, P.185, T.186, V.187 Ligands: EDO.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.160, A:V.187 EDO.12: 5 residues within 4Å: Chain B: G.244, A.246, R.273, L.274, G.275 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.273, B:G.275 EDO.13: 4 residues within 4Å: Chain B: H.44, S.196, S.197 Ligands: 0W1.10 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.197, B:S.197 Water bridges: B:K.160, B:S.197 EDO.14: 8 residues within 4Å: Chain B: M.109, Y.110, G.113, L.114, R.115, T.116, T.117, K.145 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.115, B:K.145, B:K.145 Water bridges: B:D.112

3 x 0W1: 1,3-dimethyl-1H-thieno[2,3-c]pyrazole-5-carboxylic acid(Non-covalent)

0W1.5: 8 residues within 4Å: Chain A: R.188, G.192, S.214, L.217, T.218, D.281, I.283 Ligands: EOH.2 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.218 pi-Cation interactions: A:R.188 0W1.10: 13 residues within 4Å: Chain B: H.44, G.46, H.47, A.49, L.50, G.158, K.160, V.184, P.185, T.186, V.187, M.195 Ligands: EDO.13 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:K.160, B:T.186, B:M.195 Hydrogen bonds: B:V.187 Water bridges: B:M.40 Salt bridges: B:H.47 0W1.11: 7 residues within 4Å: Chain B: R.188, G.192, S.214, L.217, T.218, D.281, I.283 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.218 pi-Cation interactions: B:R.188

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 1 residues within 4Å: Chain A: P.133 No protein-ligand interaction detected (PLIP) GOL.19: 6 residues within 4Å: Chain B: P.38, M.40, F.67, Q.72, V.142, L.146 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:F.67 Water bridges: B:T.39, B:M.40, B:F.67, B:Q.72, B:Q.164, B:Q.164

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Silvestre, H.L. et al., Integrated biophysical approach to fragment screening and validation for fragment-based lead discovery. Proc.Natl.Acad.Sci.USA (2013)

Release Date

2013-06-26

Peptides

Pantothenate synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Pantothenate synthetase

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