SMTL ID : 5drq.1

Crystal structure of the Pseudomonas aeruginosa LpxC/LPC-040 complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.63 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.78, H.237, D.241 Ligands: 5EM.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.78, A:H.237, A:D.241, A:D.241 ZN.2: 2 residues within 4Å: Chain A: H.162, E.219 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.162, A:E.219, A:E.219

1 x 5EM: N-[(2S)-3-amino-1-(hydroxyamino)-3-methyl-1-oxobutan-2-yl]-4-[4-(4-aminophenyl)buta-1,3-diyn-1-yl]benzamide(Non-covalent)

5EM.3: 18 residues within 4Å: Chain A: M.62, E.77, H.78, T.190, F.191, I.197, L.200, R.201, G.209, S.210, V.211, H.237, D.241, H.264 Ligands: ZN.1, NO3.4, NO3.7, NO3.11 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:T.190, A:I.197, A:I.197, A:I.197, A:L.200 Hydrogen bonds: A:M.62, A:E.77, A:T.190, A:T.190 Water bridges: A:F.191, A:R.201

29 x NO3: NITRATE ION(Non-functional Binders)

NO3.4: 6 residues within 4Å: Chain A: T.61, K.238, G.263, H.264 Ligands: 5EM.3, NO3.7 Ligand excluded by PLIP NO3.5: 3 residues within 4Å: Chain A: V.137, E.138, Q.269 Ligand excluded by PLIP NO3.6: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NO3.7: 5 residues within 4Å: Chain A: F.160, F.191, K.238 Ligands: 5EM.3, NO3.4 Ligand excluded by PLIP NO3.8: 7 residues within 4Å: Chain A: E.139, K.142, S.262, G.263, H.264, A.265, L.266 Ligand excluded by PLIP NO3.9: 4 residues within 4Å: Chain A: I.158, D.159, F.160, K.261 Ligand excluded by PLIP NO3.10: 2 residues within 4Å: Chain A: R.189, R.229 Ligand excluded by PLIP NO3.11: 3 residues within 4Å: Chain A: E.198, R.201 Ligands: 5EM.3 Ligand excluded by PLIP NO3.12: 6 residues within 4Å: Chain A: F.152, F.176, S.177, P.293, I.294, S.295 Ligand excluded by PLIP NO3.13: 8 residues within 4Å: Chain A: I.158, R.168, T.169, Q.170, D.232, E.233, F.234, V.235 Ligand excluded by PLIP NO3.14: 4 residues within 4Å: Chain A: R.221, V.222, L.223 Ligands: NO3.15 Ligand excluded by PLIP NO3.15: 3 residues within 4Å: Chain A: L.223, E.225 Ligands: NO3.14 Ligand excluded by PLIP NO3.16: 3 residues within 4Å: Chain A: R.133, E.134, P.148 Ligand excluded by PLIP NO3.17: 2 residues within 4Å: Chain A: Y.25, S.96 Ligand excluded by PLIP NO3.18: 4 residues within 4Å: Chain A: R.143, V.145, R.258, F.260 Ligand excluded by PLIP NO3.19: 4 residues within 4Å: Chain A: Y.230, E.231, D.232, K.236 Ligand excluded by PLIP NO3.20: 5 residues within 4Å: Chain A: H.19, M.62, L.200, L.205, A.206 Ligand excluded by PLIP NO3.21: 7 residues within 4Å: Chain A: E.59, T.60, T.61, M.62, S.63, T.65 Ligands: NO3.29 Ligand excluded by PLIP NO3.22: 3 residues within 4Å: Chain A: Q.269, R.272, T.273 Ligand excluded by PLIP NO3.23: 5 residues within 4Å: Chain A: T.285, F.286, E.287, D.288, T.291 Ligand excluded by PLIP NO3.24: 2 residues within 4Å: Chain A: K.132, R.133 Ligand excluded by PLIP NO3.25: 5 residues within 4Å: Chain A: M.1, A.125, T.285, F.286, E.287 Ligand excluded by PLIP NO3.26: 3 residues within 4Å: Chain A: V.283, V.284, T.285 Ligand excluded by PLIP NO3.27: 4 residues within 4Å: Chain A: R.41, D.70, V.71, K.72 Ligand excluded by PLIP NO3.28: 6 residues within 4Å: Chain A: R.53, A.54, E.55, L.248, L.249, I.275 Ligand excluded by PLIP NO3.29: 4 residues within 4Å: Chain A: E.59, T.60, T.61 Ligands: NO3.21 Ligand excluded by PLIP NO3.30: 4 residues within 4Å: Chain A: R.168, V.222, G.227, L.228 Ligand excluded by PLIP NO3.31: 2 residues within 4Å: Chain A: L.44, D.45 Ligand excluded by PLIP NO3.32: 4 residues within 4Å: Chain A: D.159, F.160, D.161, H.162 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, C.J. et al., Drug design from the cryptic inhibitor envelope. Nat Commun (2016)

Release Date

2016-03-09

Peptides

UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase

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