SMTL ID : 4muh.1 (1 other biounit)

Crystal structure of pantothenate synthetase in complex with 2-(2-(5-acetamido-1,3,4-thiadiazol-2-ylsulfonylcarbamoyl)-5-methoxy-1H-indol-1-yl)acetic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

homo-dimer

Ligands

4 x EOH: ETHANOL(Non-functional Binders)

EOH.1: 5 residues within 4Å: Chain A: L.114, R.115, T.117 Chain B: Q.119, P.120 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:T.117, B:Q.119 Hydrogen bonds: A:L.114 EOH.2: 2 residues within 4Å: Chain A: A.215, T.218 No protein-ligand interaction detected (PLIP) EOH.7: 2 residues within 4Å: Chain A: M.71, L.114 No protein-ligand interaction detected (PLIP) EOH.15: 3 residues within 4Å: Chain A: P.17, A.21 Chain B: N.176 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:N.176

3 x 2DN: [2-({[5-(acetylamino)-1,3,4-thiadiazol-2-yl]sulfonyl}carbamoyl)-5-methoxy-1H-indol-1-yl]acetic acid(Non-covalent)

2DN.3: 20 residues within 4Å: Chain A: P.38, T.39, M.40, H.44, G.46, H.47, L.50, Y.82, H.135, K.160, D.161, Q.164, V.184, P.185, T.186, V.187, M.195, S.196, S.197 Ligands: EDO.5 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:K.160 Hydrogen bonds: A:M.40, A:Q.164, A:Q.164, A:V.187, A:S.197 Water bridges: A:Q.72, A:Q.72, A:Q.72, A:Y.82, A:Y.82 Salt bridges: A:H.44, A:K.160 pi-Stacking: A:H.44 2DN.9: 18 residues within 4Å: Chain B: P.38, T.39, M.40, H.44, G.46, H.47, L.50, H.135, V.139, D.161, Q.164, P.185, T.186, V.187, M.195, S.196, S.197 Ligands: EDO.12 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:V.139, B:T.186 Hydrogen bonds: B:M.40, B:H.47, B:Q.164, B:Q.164, B:V.187, B:S.196, B:S.197 Water bridges: B:S.197, B:S.197 Salt bridges: B:H.44 pi-Stacking: B:H.44, B:H.44 2DN.14: 6 residues within 4Å: Chain B: R.56, V.57, P.58, R.154, F.156, V.182 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:P.58 Hydrogen bonds: B:R.154 Salt bridges: B:R.154

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

EDO.4: 9 residues within 4Å: Chain A: M.109, Y.110, G.113, L.114, R.115, T.116, T.117, K.145 Chain B: D.174 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.115, A:K.145, A:K.145 Water bridges: A:D.112 EDO.5: 6 residues within 4Å: Chain A: P.38, T.39, M.40, Q.72, V.142 Ligands: 2DN.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.72, A:Q.72 Water bridges: A:Q.164 EDO.6: 5 residues within 4Å: Chain A: A.53, V.57, R.154, F.156, V.182 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.154 EDO.8: 7 residues within 4Å: Chain A: L.147, Q.148, L.177, D.178, V.179 Chain B: Q.148, R.151 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.148, B:R.151, A:D.178 EDO.10: 9 residues within 4Å: Chain A: D.174 Chain B: M.109, Y.110, G.113, L.114, R.115, T.116, T.117, K.145 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Water bridges: A:A.173, A:A.173, A:D.174, B:D.112 Hydrogen bonds: B:R.115, B:K.145 EDO.11: 4 residues within 4Å: Chain B: F.6, A.26, L.27, T.30 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.6, B:T.30 Water bridges: B:F.6 EDO.12: 6 residues within 4Å: Chain B: P.38, T.39, M.40, N.69, V.143 Ligands: 2DN.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.38 EDO.13: 5 residues within 4Å: Chain B: G.244, A.246, R.273, L.274, G.275 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.273, B:G.275 Water bridges: B:Q.206

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hung, A.W. et al., Optimization of Inhibitors of Mycobacterium tuberculosis Pantothenate Synthetase Based on Group Efficiency Analysis. Chemmedchem (2016)

Release Date

2014-08-27

Peptides

Pantothenate synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Pantothenate synthetase

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