SMTL ID : 3ivc.1 (1 other biounit)

Crystal structure of pantothenate synthetase in complex with 2-(2-((benzofuran-2-ylmethoxy)carbonyl)-5-methoxy-1H-indol-1-yl)acetic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.13 Å

Oligo State

homo-dimer

Ligands

2 x FG4: {2-[(1-benzofuran-2-ylmethoxy)carbonyl]-5-methoxy-1H-indol-1-yl}acetic acid(Non-covalent)

FG4.1: 20 residues within 4Å: Chain A: P.38, T.39, M.40, H.44, G.46, H.47, L.50, Q.72, V.139, V.143, K.160, D.161, Q.164, V.184, P.185, T.186, V.187, M.195, S.196, S.197 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:P.38, A:L.50, A:V.139, A:V.143, A:T.186 Hydrogen bonds: A:V.187, A:S.197 Water bridges: A:Q.164, A:S.197 Salt bridges: A:H.44, A:H.47, A:H.47, A:K.160 pi-Stacking: A:H.44, A:H.44 FG4.9: 21 residues within 4Å: Chain B: P.38, T.39, M.40, H.44, G.46, H.47, L.50, Q.72, V.139, V.142, V.143, G.158, K.160, Q.164, V.184, P.185, T.186, V.187, M.195, S.196, S.197 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.50, B:V.139, B:V.142, B:V.143, B:K.160 Hydrogen bonds: B:V.187, B:S.197 Salt bridges: B:H.44, B:H.47, B:H.47 pi-Stacking: B:H.44 pi-Cation interactions: B:H.44

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: L.147, Q.148, R.151, P.152, L.177, D.178, V.179 Chain B: Q.148, R.151 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Q.148, B:R.151, A:L.147, A:Q.148, A:P.152 GOL.3: 4 residues within 4Å: Chain A: I.3, P.4, A.5, F.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.4, A:F.6 GOL.4: 10 residues within 4Å: Chain A: M.109, Y.110, P.111, D.112, G.113, L.114, R.115, T.116, K.145 Chain B: D.174 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.112, A:R.115, A:K.145, A:K.145 GOL.5: 1 residues within 4Å: Chain A: R.200 No protein-ligand interaction detected (PLIP) GOL.6: 5 residues within 4Å: Chain A: N.176, D.178 Chain B: A.21, I.149 Ligands: EOH.15 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.176, A:D.178 GOL.10: 5 residues within 4Å: Chain B: G.244, A.246, R.273, L.274, G.275 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.244, B:R.273, B:G.275, B:G.275 Water bridges: B:Q.206 GOL.11: 5 residues within 4Å: Chain A: P.17, Q.148, I.149 Chain B: N.176, D.178 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.176, A:Q.148 GOL.13: 10 residues within 4Å: Chain A: D.174 Chain B: M.109, Y.110, P.111, D.112, G.113, L.114, R.115, T.116, K.145 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.112, B:D.112, B:R.115, B:T.116, B:K.145, B:K.145 GOL.14: 4 residues within 4Å: Chain B: E.189, M.195, S.196, N.199 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.196, B:N.199

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

SO4.7: 4 residues within 4Å: Chain A: P.120, G.121, A.124, A.125 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.120 SO4.8: 4 residues within 4Å: Chain A: P.261, G.264, S.265, F.290 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.265

2 x EOH: ETHANOL(Non-functional Binders)

EOH.12: 5 residues within 4Å: Chain B: L.147, R.151, P.152, D.178, V.179 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:R.151, B:V.179 Hydrogen bonds: B:R.151, B:D.178, A:Q.148 EOH.15: 6 residues within 4Å: Chain A: D.178 Chain B: A.21, Q.148, I.149, R.151 Ligands: GOL.6 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:A.21 Hydrogen bonds: A:D.178

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hung, A.W. et al., Application of fragment growing and fragment linking to the discovery of inhibitors of Mycobacterium tuberculosis pantothenate synthetase. Angew.Chem.Int.Ed.Engl. (2009)

Release Date

2009-10-13

Peptides

Pantothenate synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Pantothenate synthetase

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