SMTL ID : 5jwc.1

Structure of NDH2 from plasmodium falciparum in complex with RYL-552

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 32 residues within 4Å: Chain A: G.35, S.36, G.37, W.38, G.39, I.57, S.58, P.59, R.60, T.66, P.67, E.104, C.105, A.135, V.136, G.137, V.155, T.199, L.304, G.341, D.342, P.422, T.423, A.424, Q.425, A.427, Y.492 Ligands: MG.2, MG.3, MG.4, MG.5, TRT.8 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:T.199 Hydrogen bonds: A:S.36, A:S.36, A:W.38, A:G.39, A:S.58, A:T.66, A:T.66, A:C.105, A:C.105, A:G.137, A:D.342, A:P.422, A:A.424, A:Q.425, A:Y.492 Water bridges: A:R.60, A:R.60, A:K.156, A:T.199, A:A.427 FAD.12: 32 residues within 4Å: Chain B: G.35, S.36, G.37, W.38, G.39, I.57, S.58, P.59, R.60, T.66, P.67, E.104, C.105, A.135, V.136, G.137, V.155, T.199, L.304, G.341, D.342, P.422, T.423, A.424, Q.425, A.427, Y.492 Ligands: MG.13, MG.14, MG.15, MG.16, TRT.19 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:T.199 Hydrogen bonds: B:S.36, B:S.36, B:W.38, B:G.39, B:S.58, B:T.66, B:C.105, B:C.105, B:G.137, B:D.342, B:P.422, B:A.424, B:Q.425 Water bridges: B:R.60, B:R.60, B:E.104, B:K.156, B:K.156, B:K.156, B:Q.425, B:Q.425, B:A.427, B:Y.492

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 8 residues within 4Å: Chain A: A.135, V.136, G.137, I.340, G.341, D.342, C.343 Ligands: FAD.1 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:I.340, FAD.1 MG.3: 7 residues within 4Å: Chain A: G.35, G.37, W.38, G.39, G.40, A.135 Ligands: FAD.1 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:A.135, FAD.1 MG.4: 6 residues within 4Å: Chain A: G.37, W.38, R.60, F.63, T.64 Ligands: FAD.1 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.64, H2O.5 MG.5: 4 residues within 4Å: Chain A: G.137, A.138, K.156 Ligands: FAD.1 No protein-ligand interaction detected (PLIP) MG.13: 8 residues within 4Å: Chain B: A.135, V.136, G.137, I.340, G.341, D.342, C.343 Ligands: FAD.12 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:I.340, FAD.12 MG.14: 8 residues within 4Å: Chain B: G.35, S.36, G.37, W.38, G.39, G.40, A.135 Ligands: FAD.12 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:A.135, FAD.12 MG.15: 7 residues within 4Å: Chain B: G.37, W.38, R.60, F.63, T.64, T.66 Ligands: FAD.12 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.64, H2O.13 MG.16: 5 residues within 4Å: Chain B: G.137, A.138, K.156, D.342 Ligands: FAD.12 No protein-ligand interaction detected (PLIP)

6 x TRT: FRAGMENT OF TRITON X-100(Non-covalent)

TRT.6: 6 residues within 4Å: Chain A: I.493, Q.494, L.497, W.499, R.502 Ligands: TRT.18 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.493, A:Q.494 Hydrogen bonds: A:R.502, A:R.502 TRT.7: 5 residues within 4Å: Chain A: Y.515 Chain B: I.493, W.499, F.503, F.506 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.493, B:W.499, B:F.503, B:F.503, B:F.506 TRT.8: 13 residues within 4Å: Chain A: W.38, A.424, Q.425, K.428, K.458, G.459, L.461, V.490, V.491, Y.492, Q.494, L.495 Ligands: FAD.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.490, A:V.491, A:Q.494, A:L.495 Hydrogen bonds: A:Q.425 TRT.17: 5 residues within 4Å: Chain B: I.493, Q.494, L.497, W.499, R.502 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.493, B:Q.494 Hydrogen bonds: B:R.502, B:R.502 TRT.18: 6 residues within 4Å: Chain A: W.499, R.502, F.503, F.506 Chain B: Y.515 Ligands: TRT.6 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.503, A:F.506, A:F.506, A:F.506 Water bridges: A:W.499 Hydrogen bonds: B:Y.515 TRT.19: 11 residues within 4Å: Chain B: W.38, Q.425, K.428, K.458, G.459, V.490, V.491, Y.492, Q.494, L.495 Ligands: FAD.12 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.490, B:V.491, B:V.491, B:L.495 Water bridges: B:Q.425, B:Q.425, B:Q.425, B:Q.425

4 x 4W0: 5-fluoro-3-methyl-2-{4-[4-(trifluoromethoxy)benzyl]phenyl}quinolin-4(1H)-one(Non-covalent)

4W0.9: 15 residues within 4Å: Chain A: Y.62, V.79, N.80, I.158, D.159, L.162 Chain B: L.72, G.75, L.77, S.78, L.162, R.165, P.518, I.520, K.521 12 PLIP interactions: 5 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:L.72, B:L.162, B:P.518, B:I.520, A:V.79, A:V.79, A:I.158, A:D.159, A:L.162 Halogen bonds: B:K.521 Hydrogen bonds: A:N.80 Water bridges: A:D.159 4W0.10: 15 residues within 4Å: Chain A: L.72, G.75, L.77, S.78, L.162, R.165, P.518, I.520, K.521 Chain B: Y.62, V.79, N.80, I.158, D.159, L.162 13 PLIP interactions: 7 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:V.79, B:V.79, B:I.158, B:D.159, B:L.162, A:L.72, A:L.162, A:P.518, A:I.520, A:I.520 Hydrogen bonds: B:Y.62, B:N.80 Halogen bonds: A:K.521 4W0.11: 11 residues within 4Å: Chain A: E.206, D.209, N.212, K.213, Y.463, N.466, H.467, S.485, W.488, K.489, R.517 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:D.209, A:N.212, A:K.213, A:K.213 Hydrogen bonds: A:D.209, A:S.485, A:K.489 Water bridges: A:T.76 pi-Stacking: A:Y.463, A:W.488 Halogen bonds: A:N.466, A:S.485 4W0.20: 11 residues within 4Å: Chain B: E.206, D.209, N.212, K.213, Y.463, N.466, H.467, S.485, W.488, K.489, R.517 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:D.209, B:N.212, B:K.213 Hydrogen bonds: B:D.209, B:D.209, B:S.485, B:K.489 Water bridges: B:Y.463 pi-Stacking: B:Y.463, B:W.488 Halogen bonds: B:S.485

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, Y. et al., Target Elucidation by Cocrystal Structures of NADH-Ubiquinone Oxidoreductase of Plasmodium falciparum (PfNDH2) with Small Molecule To Eliminate Drug-Resistant Malaria. J. Med. Chem. (2017)

Release Date

2017-03-22

Peptides

NADH dehydrogenase, putative: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

NADH dehydrogenase, putative

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