SMTL ID : 5lbz.1

Structure of the human quinone reductase 2 (NQO2) in complex with pacritinib

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 26 residues within 4Å: Chain A: H.12, K.16, S.17, F.18, N.19, S.21, P.103, L.104, Y.105, W.106, F.107, T.148, T.149, G.150, G.151, Y.156, P.193, E.194, E.198, R.201, K.202, V.205 Chain B: N.67, Y.68, D.118 Ligands: 6T3.7 25 PLIP interactions: 21 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:Y.105, A:Y.105, A:Y.105, B:Y.68 Hydrogen bonds: A:F.18, A:N.19, A:N.19, A:S.21, A:S.21, A:L.104, A:L.104, A:W.106, A:F.107, A:T.148, A:T.148, A:G.150, A:G.151, A:Y.156, A:Y.156 Water bridges: A:K.16, A:E.194, B:N.67, B:N.67, B:N.67 Salt bridges: A:H.12 FAD.6: 26 residues within 4Å: Chain A: Y.68, G.69, D.118 Chain B: H.12, K.16, S.17, F.18, N.19, S.21, P.103, L.104, Y.105, W.106, F.107, T.148, T.149, G.150, G.151, Y.156, P.193, E.194, E.198, R.201, K.202, V.205 Ligands: 6T3.2 23 PLIP interactions: 21 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.105, B:Y.105, B:Y.105, A:Y.68 Hydrogen bonds: B:F.18, B:N.19, B:N.19, B:S.21, B:S.21, B:L.104, B:L.104, B:W.106, B:F.107, B:T.148, B:T.148, B:G.150, B:G.151, B:Y.156, B:Y.156, A:N.67 Water bridges: B:K.16 Salt bridges: B:H.12 pi-Stacking: B:F.18

2 x 6T3: 11-(2-pyrrolidin-1-yl-ethoxy)-14,19-dioxa-5,7,26-triaza-tetracyclo[19.3.1.1(2,6).1(8,12)]heptacosa-1(25),2(26),3,5,8,10,12(27),16,21,23-decaene(Non-covalent)

6T3.2: 13 residues within 4Å: Chain A: F.127, I.129, G.175, F.179 Chain B: W.106, F.107, G.150, G.151, M.155, N.162, E.194, I.195 Ligands: FAD.6 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:W.106, B:F.107, B:I.195, A:F.127, A:I.129 Hydrogen bonds: B:N.162 pi-Stacking: B:W.106, A:F.179 Water bridges: A:Q.123 6T3.7: 14 residues within 4Å: Chain A: W.106, F.107, G.150, G.151, M.155, Y.156, N.162, E.194 Chain B: F.127, I.129, F.132, G.175, F.179 Ligands: FAD.1 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:W.106, A:F.107, B:F.132 Hydrogen bonds: A:N.162 pi-Stacking: A:W.106, B:F.179

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

SO4.3: 3 residues within 4Å: Chain A: V.70, H.73, Q.123 7 PLIP interactions: 7 interactions with chain A Water bridges: A:H.73, A:E.74, A:Q.123, A:Q.123, A:Q.123, A:Q.123 Salt bridges: A:H.73 SO4.4: 4 residues within 4Å: Chain A: P.222, T.224, H.226, W.227 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.224 Salt bridges: A:H.226 SO4.8: 4 residues within 4Å: Chain A: N.46, E.48, R.50 Chain B: R.50 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.46 Salt bridges: A:R.50, B:R.50 SO4.9: 1 residues within 4Å: Chain B: R.166 4 PLIP interactions: 4 interactions with chain B Water bridges: B:S.165, B:R.166, B:R.166 Salt bridges: B:R.166

2 x ZN: ZINC ION(Non-covalent)

ZN.5: 3 residues within 4Å: Chain A: H.174, H.178, C.223 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.174, A:H.178, A:C.223, A:C.223 ZN.10: 3 residues within 4Å: Chain B: H.174, H.178, C.223 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.174, B:H.178, B:C.223, B:C.223

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Klaeger, S. et al., The target landscape of clinical kinase drugs. Science (2017)

Release Date

2017-11-29

Peptides

Ribosyldihydronicotinamide dehydrogenase [quinone]: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ribosyldihydronicotinamide dehydrogenase [quinone]

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