SMTL ID : 6iw7.5 (6 other biounits)

structural insights into Mycobacterium tuberculosis ClpP1P2 inhibition by Cediranib: implications for developing antimicrobial agents targeting Clp protease

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.69 Å

Oligo State

hetero-1-1-mer

Ligands

2 x S0R: (2S)-2-benzamido-4-methyl-pentanoic acid(Non-covalent)

S0R.1: 11 residues within 4Å: Chain A: G.69, G.70, F.71, L.74, S.98, A.99, H.123, P.125, S.126, M.152 Ligands: LEU.2 7 PLIP interactions: 6 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:F.71, A:L.74, A:A.99 Hydrogen bonds: A:G.69, A:F.71, A:S.126, L.2 S0R.4: 8 residues within 4Å: Chain A: F.135 Chain B: G.63, S.64, I.65, P.119, L.120, F.137 Ligands: LEU.5 7 PLIP interactions: 5 interactions with chain B, 1 Ligand-Ligand interactions, 1 interactions with chain A Hydrophobic interactions: B:I.65, B:F.137 Hydrogen bonds: B:I.65, B:L.120, B:L.120, L.5 pi-Stacking: A:F.135

2 x LEU: LEUCINE(Non-covalent)

LEU.2: 7 residues within 4Å: Chain A: F.71, P.125, S.126, L.127, I.145, M.148 Ligands: S0R.1 5 PLIP interactions: 5 interactions with chain A, Hydrophobic interactions: A:F.71, A:P.125, A:L.127, A:I.145 Hydrogen bonds: A:S.126 LEU.5: 9 residues within 4Å: Chain B: G.62, G.63, I.65, S.92, M.93, H.117, L.120, M.144 Ligands: S0R.4 6 PLIP interactions: 6 interactions with chain B, Hydrogen bonds: B:G.63, B:G.63, B:G.63, B:S.92, B:M.93 Salt bridges: B:H.117

1 x AV3: 4-[(4-fluoro-2-methyl-3H-indol-5-yl)oxy]-6-methoxy-7-[3-(pyrrolidin-1-yl)propoxy]quinazoline(Non-covalent)

AV3.3: 6 residues within 4Å: Chain B: G.88, M.89, H.111, A.112, R.113, W.168 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:R.113 pi-Stacking: B:W.168 pi-Cation interactions: B:R.113

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bao, R. et al., structural insights into Mycobacterium tuberculosis ClpP1P2 inhibition by Cediranib: implications for developing antimicrobial agents targeting Clp protease. To Be Published

Release Date

2020-01-01

Peptides

ATP-dependent Clp protease proteolytic subunit 2: A
ATP-dependent Clp protease proteolytic subunit 1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
J

B
K

ATP-dependent Clp protease proteolytic subunit 2

ATP-dependent Clp protease proteolytic subunit 1

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