SMTL ID : 9dc8.1

Mtb GuaB dCBS in complex with inhibitor G1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

4 x IMP: INOSINIC ACID(Non-covalent)

IMP.1: 22 residues within 4Å: Chain A: S.98, M.100, N.203, G.228, S.229, I.230, C.231, D.264, G.265, G.266, M.285, L.286, G.287, S.288, Y.311, G.313, M.314, G.315, S.316, E.348, G.349 Ligands: VOA.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:S.98, A:N.203, A:S.229, A:D.264, A:G.266, A:G.287, A:S.288, A:M.314, A:G.315, A:E.348 Water bridges: A:G.228, A:G.266, A:L.267, A:L.267 IMP.6: 22 residues within 4Å: Chain B: S.98, M.100, N.203, G.228, S.229, I.230, C.231, D.264, G.265, G.266, M.285, L.286, G.287, S.288, Y.311, G.313, M.314, G.315, S.316, E.348, G.349 Ligands: VOA.7 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:S.98, B:N.203, B:S.229, B:D.264, B:G.266, B:G.287, B:S.288, B:M.314, B:G.315, B:E.348 Water bridges: B:G.228, B:G.266, B:L.267, B:L.267 IMP.11: 22 residues within 4Å: Chain C: S.98, M.100, N.203, G.228, S.229, I.230, C.231, D.264, G.265, G.266, M.285, L.286, G.287, S.288, Y.311, G.313, M.314, G.315, S.316, E.348, G.349 Ligands: VOA.12 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:S.98, C:N.203, C:S.229, C:D.264, C:G.266, C:G.287, C:S.288, C:M.314, C:G.315, C:E.348 Water bridges: C:G.228, C:G.266, C:L.267, C:L.267 IMP.16: 22 residues within 4Å: Chain D: S.98, M.100, N.203, G.228, S.229, I.230, C.231, D.264, G.265, G.266, M.285, L.286, G.287, S.288, Y.311, G.313, M.314, G.315, S.316, E.348, G.349 Ligands: VOA.17 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:S.98, D:N.203, D:S.229, D:D.264, D:G.266, D:G.287, D:S.288, D:M.314, D:G.315, D:E.348 Water bridges: D:G.228, D:G.266, D:L.267, D:L.267

12 x VOA: N-(6-chloropyridin-3-yl)-N~2~-(1,4-dihydro-2H-pyrano[3,4-c]quinolin-9-yl)-L-alaninamide(Non-covalent)

VOA.2: 20 residues within 4Å: Chain A: A.175, N.203, G.224, V.225, G.226, T.233, M.314, G.315, M.320, L.345, V.346, E.348 Chain D: V.74, P.76, A.373, G.376, Y.377 Ligands: IMP.1, VOA.3, VOA.4 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: A:A.175, A:L.345, A:E.348, D:P.76, D:Y.377 Hydrogen bonds: A:G.226, A:E.348, D:Y.377 Halogen bonds: D:V.74 VOA.3: 13 residues within 4Å: Chain A: R.123, N.124, V.151, D.173, T.174, A.175, N.179, A.319, M.320, L.345 Ligands: VOA.2, VOA.4, SO4.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.345 Hydrogen bonds: A:A.175 Halogen bonds: A:N.179 VOA.4: 8 residues within 4Å: Chain A: V.151, D.154, L.345 Chain D: V.75, P.76 Ligands: VOA.2, VOA.3, SO4.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.151 VOA.7: 20 residues within 4Å: Chain B: A.175, N.203, G.224, V.225, G.226, T.233, M.314, G.315, M.320, L.345, V.346, E.348 Chain C: V.74, P.76, A.373, G.376, Y.377 Ligands: IMP.6, VOA.8, VOA.9 9 PLIP interactions: 4 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:P.76, C:Y.377, B:A.175, B:L.345, B:E.348 Hydrogen bonds: C:Y.377, B:G.226, B:E.348 Halogen bonds: C:V.74 VOA.8: 13 residues within 4Å: Chain B: R.123, N.124, V.151, D.173, T.174, A.175, N.179, A.319, M.320, L.345 Ligands: VOA.7, VOA.9, SO4.10 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.345 Hydrogen bonds: B:A.175 Halogen bonds: B:N.179 VOA.9: 8 residues within 4Å: Chain B: V.151, D.154, L.345 Chain C: V.75, P.76 Ligands: VOA.7, VOA.8, SO4.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.151 VOA.12: 20 residues within 4Å: Chain A: V.74, P.76, A.373, G.376, Y.377 Chain C: A.175, N.203, G.224, V.225, G.226, T.233, M.314, G.315, M.320, L.345, V.346, E.348 Ligands: IMP.11, VOA.13, VOA.14 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:A.175, C:L.345, C:E.348, A:P.76, A:Y.377 Hydrogen bonds: C:G.226, C:E.348, A:Y.377 Halogen bonds: A:V.74 VOA.13: 13 residues within 4Å: Chain C: R.123, N.124, V.151, D.173, T.174, A.175, N.179, A.319, M.320, L.345 Ligands: VOA.12, VOA.14, SO4.15 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.345 Hydrogen bonds: C:A.175 Halogen bonds: C:N.179 VOA.14: 8 residues within 4Å: Chain A: V.75, P.76 Chain C: V.151, D.154, L.345 Ligands: VOA.12, VOA.13, SO4.15 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:V.151 VOA.17: 20 residues within 4Å: Chain B: V.74, P.76, A.373, G.376, Y.377 Chain D: A.175, N.203, G.224, V.225, G.226, T.233, M.314, G.315, M.320, L.345, V.346, E.348 Ligands: IMP.16, VOA.18, VOA.19 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain D Hydrophobic interactions: B:P.76, B:Y.377, D:A.175, D:L.345, D:E.348 Hydrogen bonds: B:Y.377, D:G.226, D:E.348 Halogen bonds: B:V.74 VOA.18: 13 residues within 4Å: Chain D: R.123, N.124, V.151, D.173, T.174, A.175, N.179, A.319, M.320, L.345 Ligands: VOA.17, VOA.19, SO4.20 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:L.345 Hydrogen bonds: D:A.175 Halogen bonds: D:N.179 VOA.19: 8 residues within 4Å: Chain B: V.75, P.76 Chain D: V.151, D.154, L.345 Ligands: VOA.17, VOA.18, SO4.20 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:V.151

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

SO4.5: 5 residues within 4Å: Chain A: R.123, G.150, V.151 Ligands: VOA.3, VOA.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.151, A:V.151 Water bridges: A:R.123 Salt bridges: A:R.123 SO4.10: 5 residues within 4Å: Chain B: R.123, G.150, V.151 Ligands: VOA.8, VOA.9 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.151, B:V.151 Water bridges: B:R.123 Salt bridges: B:R.123 SO4.15: 5 residues within 4Å: Chain C: R.123, G.150, V.151 Ligands: VOA.13, VOA.14 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:V.151, C:V.151 Water bridges: C:R.123 Salt bridges: C:R.123 SO4.20: 5 residues within 4Å: Chain D: R.123, G.150, V.151 Ligands: VOA.18, VOA.19 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:V.151, D:V.151 Water bridges: D:R.123 Salt bridges: D:R.123

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, Y. et al., Discovery of potent dihydro-oxazinoquinolinone inhibitors of GuaB for the treatment of tuberculosis. Bioorg.Med.Chem.Lett. (2024)

Release Date

2024-11-27

Peptides

Inosine-5'-monophosphate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Inosine-5'-monophosphate dehydrogenase

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