SMTL ID : 8u0q.1

Co-crystal structure of optimized analog TDI-13537 provided new insights into the potency determinants of the sulfonamide inhibitor series

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

homo-dimer

Ligands

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 39 residues within 4Å: Chain A: L.11, G.12, G.14, P.15, G.16, G.17, V.34, E.35, P.36, Y.38, G.41, V.42, C.43, V.46, G.47, C.48, S.51, K.52, Y.114, G.115, A.143, T.144, G.145, Y.163, I.184, F.188, Y.278, G.310, D.311, Q.317, L.318, A.319, H.320, A.322, F.352 Chain B: H.445, P.446 Ligands: GOL.6, GOL.7 22 PLIP interactions: 21 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.42, A:Y.163, A:I.184, A:F.188 Hydrogen bonds: A:G.14, A:G.16, A:G.17, A:V.42, A:C.43, A:K.52, A:G.115, A:G.115, A:D.311, A:Q.317, A:A.319, A:H.320, B:H.445 Water bridges: A:G.145, A:S.146, A:S.146, A:S.146, A:V.312 FAD.26: 38 residues within 4Å: Chain A: H.445, P.446 Chain B: L.11, G.12, G.14, P.15, G.16, G.17, V.34, E.35, P.36, Y.38, G.41, V.42, C.43, V.46, G.47, C.48, S.51, K.52, Y.114, G.115, A.143, T.144, G.145, Y.163, I.184, F.188, Y.278, G.310, D.311, Q.317, L.318, A.319, H.320, A.322, F.352 Ligands: GOL.29 23 PLIP interactions: 22 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.42, B:Y.163, B:Y.163, B:I.184, B:F.188 Hydrogen bonds: B:G.14, B:G.16, B:G.17, B:V.42, B:C.43, B:K.52, B:G.115, B:G.115, B:D.311, B:Q.317, B:A.319, B:H.320, A:H.445 Water bridges: B:G.145, B:S.146, B:S.146, B:S.146, B:V.312

2 x U4I: N-(3-acetamidophenyl)-N~2~-[3-(difluoromethyl)-5-methylbenzene-1-sulfonyl]-N~2~-methylglycinamide

U4I.2: 18 residues within 4Å: Chain A: F.379, A.383, N.384, A.385, H.445, E.450, E.454, N.465, F.466 Chain B: Y.18, L.44, R.95, G.98, F.101, K.105, E.323 Ligands: GOL.21, GOL.40 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.466, A:F.466, B:F.101 Hydrogen bonds: A:N.465, A:F.466, B:R.95 Halogen bonds: A:N.384 U4I.23: 17 residues within 4Å: Chain A: Y.18, L.44, R.95, G.98, V.99, F.101, L.102, E.323 Chain B: F.379, A.383, N.384, A.385, H.445, E.450, E.454, N.465, F.466 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:F.101, A:L.102, B:F.466, B:F.466 Hydrogen bonds: A:R.95, B:N.465, B:F.466 Halogen bonds: B:N.384

36 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 9 residues within 4Å: Chain A: Q.453, E.454, H.457, I.464, N.465 Chain B: E.323, A.324, V.327 Ligands: GOL.12 Ligand excluded by PLIP GOL.4: 8 residues within 4Å: Chain A: K.52, L.55, R.56, F.352, N.356, D.417 Chain B: K.386, V.390 Ligand excluded by PLIP GOL.5: 6 residues within 4Å: Chain A: A.25, L.29, S.30, T.31, N.106, K.107 Ligand excluded by PLIP GOL.6: 6 residues within 4Å: Chain A: K.37, Y.38, V.42, S.146, S.147 Ligands: FAD.1 Ligand excluded by PLIP GOL.7: 6 residues within 4Å: Chain A: A.183, I.184, F.271, Q.317, L.318 Ligands: FAD.1 Ligand excluded by PLIP GOL.8: 2 residues within 4Å: Chain A: G.304, H.305 Ligand excluded by PLIP GOL.9: 6 residues within 4Å: Chain A: L.172, P.173, K.174, Y.195, G.196 Ligands: GOL.22 Ligand excluded by PLIP GOL.10: 6 residues within 4Å: Chain A: S.147, A.272, P.273, N.274, V.275, E.276 Ligand excluded by PLIP GOL.11: 5 residues within 4Å: Chain A: V.295, D.296, D.297, L.315, G.342 Ligand excluded by PLIP GOL.12: 8 residues within 4Å: Chain A: A.439, R.440, Q.453, H.457 Chain B: A.324, V.327, V.328 Ligands: GOL.3 Ligand excluded by PLIP GOL.13: 3 residues within 4Å: Chain A: N.211, R.345, R.349 Ligand excluded by PLIP GOL.14: 2 residues within 4Å: Chain A: Y.298, R.300 Ligand excluded by PLIP GOL.15: 6 residues within 4Å: Chain A: K.193, D.198, V.199, T.200, G.228, T.230 Ligand excluded by PLIP GOL.16: 6 residues within 4Å: Chain A: G.294, V.295, D.296, R.300, T.301, N.302 Ligand excluded by PLIP GOL.17: 5 residues within 4Å: Chain A: S.436, E.437, R.440 Chain B: E.337, W.431 Ligand excluded by PLIP GOL.18: 4 residues within 4Å: Chain A: D.343, M.346, Y.372, Q.429 Ligand excluded by PLIP GOL.19: 10 residues within 4Å: Chain A: A.179, G.180, V.202, E.203, F.204, T.235, K.236, V.237, I.269 Ligands: GOL.20 Ligand excluded by PLIP GOL.20: 6 residues within 4Å: Chain A: G.180, G.182, E.203, P.210, I.269 Ligands: GOL.19 Ligand excluded by PLIP GOL.21: 3 residues within 4Å: Chain A: T.382, A.383 Ligands: U4I.2 Ligand excluded by PLIP GOL.22: 5 residues within 4Å: Chain A: F.79, D.80, Y.81, Y.195 Ligands: GOL.9 Ligand excluded by PLIP GOL.24: 7 residues within 4Å: Chain A: E.323, A.324 Chain B: Q.453, E.454, H.457, I.464, N.465 Ligand excluded by PLIP GOL.25: 6 residues within 4Å: Chain A: H.388 Chain B: K.90, V.91, G.94, R.95 Ligands: GOL.40 Ligand excluded by PLIP GOL.27: 5 residues within 4Å: Chain A: R.87, V.91 Chain B: H.388, P.393 Ligands: GOL.36 Ligand excluded by PLIP GOL.28: 5 residues within 4Å: Chain B: N.211, L.316, R.345, R.349 Ligands: GOL.34 Ligand excluded by PLIP GOL.29: 9 residues within 4Å: Chain B: K.52, A.183, I.184, E.187, L.318, A.350, F.352 Ligands: FAD.26, GOL.34 Ligand excluded by PLIP GOL.30: 7 residues within 4Å: Chain B: K.193, D.198, V.199, T.200, G.228, V.229, T.230 Ligand excluded by PLIP GOL.31: 3 residues within 4Å: Chain B: T.116, L.124, D.126 Ligand excluded by PLIP GOL.32: 6 residues within 4Å: Chain B: S.147, A.272, P.273, N.274, V.275, E.276 Ligand excluded by PLIP GOL.33: 3 residues within 4Å: Chain B: Q.429, R.430, D.432 Ligand excluded by PLIP GOL.34: 8 residues within 4Å: Chain B: A.183, N.211, E.212, R.349, A.350, T.351 Ligands: GOL.28, GOL.29 Ligand excluded by PLIP GOL.35: 8 residues within 4Å: Chain B: A.25, G.28, L.29, S.30, T.31, N.106, K.107, I.108 Ligand excluded by PLIP GOL.36: 5 residues within 4Å: Chain A: R.87 Chain B: D.67, A.70, G.391 Ligands: GOL.27 Ligand excluded by PLIP GOL.37: 4 residues within 4Å: Chain B: H.405, E.407, D.432, T.434 Ligand excluded by PLIP GOL.38: 6 residues within 4Å: Chain B: G.180, G.182, E.203, A.268, I.269 Ligands: GOL.39 Ligand excluded by PLIP GOL.39: 9 residues within 4Å: Chain B: G.180, V.202, E.203, F.204, T.235, K.236, V.237, I.269 Ligands: GOL.38 Ligand excluded by PLIP GOL.40: 7 residues within 4Å: Chain B: G.94, R.95, A.97, G.98, F.101 Ligands: U4I.2, GOL.25 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Michino, M. et al., Shape-Based Virtual Screening of a Billion-Compound Library Identifies Mycobacterial Lipoamide Dehydrogenase Inhibitors. Acs Bio Med Chem Au (2023)

Release Date

2024-01-03

Peptides

Dihydrolipoyl dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dihydrolipoyl dehydrogenase

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