SMTL ID : 9c1v.1

M. tuberculosis PKS13 acyltransferase (AT) domain in complex with SuFEx inhibitor CMX410

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.57 Å

Oligo State

homo-dimer

Ligands

7 x GLC- FRU: beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose(Non-covalent)

GLC-FRU.1: 9 residues within 4Å: Chain A: R.55, L.56, A.59, E.63, K.177, L.210, D.211, D.212, A.213 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:E.63, A:R.55, A:R.55, A:K.177, A:K.177, A:D.211, A:D.211, A:D.212, A:A.213 Water bridges: A:A.60 GLC-FRU.2: 11 residues within 4Å: Chain A: H.119, R.123, L.481, Y.482, G.485, H.486, D.487, L.488, D.489, I.490, R.491 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.123, A:R.123, A:L.481, A:L.488, A:L.488, A:D.489, A:I.490, A:R.491, A:R.491 Water bridges: A:D.487 GLC-FRU.3: 4 residues within 4Å: Chain A: E.289, P.312, D.313, Q.333 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Q.333, A:E.332 Hydrogen bonds: A:E.289, A:Q.333 GLC-FRU.4: 10 residues within 4Å: Chain B: R.182, N.183, E.184, V.185, L.235, H.238, H.239, T.492, L.493, S.495 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.183, B:E.184, B:E.184, B:V.185 Water bridges: B:E.108, B:E.108, B:E.108, B:L.493 GLC-FRU.5: 10 residues within 4Å: Chain B: E.101, A.104, S.105, S.106, S.109, P.500, Q.501, Y.503, A.504, N.505 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.101, B:E.101, B:N.505, B:S.106, B:S.109, B:S.109, B:N.505, B:N.505 Water bridges: B:N.505, B:N.505 GLC-FRU.6: 9 residues within 4Å: Chain B: V.157, T.158, T.159, G.160, P.161, G.485, H.486, D.487 Ligands: GLC-FRU.7 2 PLIP interactions: 2 interactions with chain B Water bridges: B:K.242 Hydrogen bonds: B:V.157, B:D.487 GLC-FRU.7: 11 residues within 4Å: Chain B: H.119, R.123, Y.482, G.485, H.486, D.487, L.488, D.489, I.490, R.491 Ligands: GLC-FRU.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.123, B:R.123, B:L.481, B:D.487, B:L.488, B:L.488, B:I.490, B:R.491, B:R.491

3 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.8: 12 residues within 4Å: Chain A: F.168, I.218, M.279, G.282, E.283, L.286, T.353, G.355, S.357, Q.361, M.362 Ligands: 01.16 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.357 1PE.9: 3 residues within 4Å: Chain A: A.188, W.189, K.192 No protein-ligand interaction detected (PLIP) 1PE.10: 7 residues within 4Å: Chain A: V.426, D.427, S.428, G.429, A.453, G.454, L.455 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.427, A:G.454

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

SO4.11: 5 residues within 4Å: Chain A: E.92, L.93, R.117, I.506, P.507 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.92 Salt bridges: A:R.117, A:R.510 SO4.12: 6 residues within 4Å: Chain A: V.157, T.158, T.159, G.160, G.485, H.486 3 PLIP interactions: 3 interactions with chain A Water bridges: A:D.487, A:D.487 Salt bridges: A:H.486 SO4.13: 2 residues within 4Å: Chain A: T.492, L.493 No protein-ligand interaction detected (PLIP) SO4.14: 4 residues within 4Å: Chain A: P.507, P.508, T.509, R.510 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.510 SO4.15: 3 residues within 4Å: Chain A: Y.203, E.219, T.220 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.219 Water bridges: A:T.220 SO4.17: 3 residues within 4Å: Chain B: R.117, N.118, K.512 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.118, B:N.118 Water bridges: B:K.512 Salt bridges: B:K.512 SO4.18: 2 residues within 4Å: Chain B: N.439, R.466 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.439 Salt bridges: B:R.466 SO4.19: 3 residues within 4Å: Chain B: Y.203, E.219, T.220 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.219

1 x 01: N-(1-{3,5-difluoro-4-[(4-{[fluorodi(hydroxy)-lambda~4~-sulfanyl]oxy}phenoxy)methyl]phenyl}-1H-1,2,4-triazol-3-yl)methanesulfonamide

01.16: 19 residues within 4Å: Chain A: F.168, Q.249, S.250, R.275, M.279, M.294, L.296, V.318, A.320, Q.324, V.326, F.347, R.349, F.351, S.357, H.358, V.441, Q.445 Ligands: 1PE.8 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.168, A:L.296, A:V.318, A:F.351 Hydrogen bonds: A:Q.324, A:R.349, A:S.357 pi-Stacking: A:F.168

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Krieger, I.K. et al., A SuFEx-based TB clinical candidate irreversibly inhibits Pks13. To Be Published

Release Date

2025-05-07

Peptides

Polyketide synthase Pks13: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Polyketide synthase Pks13

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