SMTL ID : 3vq5.1

HIV-1 IN core domain in complex with N-METHYL-1-(4-METHYL-2-PHENYL-1,3-THIAZOL-5-YL)METHANAMINE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

4 x CD: CADMIUM ION(Non-covalent)

CD.1: 4 residues within 4Å: Chain A: C.10, H.12, E.37 Ligands: CD.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.10, A:H.12, A:E.37 CD.2: 5 residues within 4Å: Chain A: C.10, E.37, D.61 Ligands: CD.1, CL.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:C.10, A:E.37, A:D.61, H2O.1, H2O.1 CD.8: 4 residues within 4Å: Chain B: C.10, H.12, E.37 Ligands: CD.9 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.10, B:H.12, B:E.37 CD.9: 5 residues within 4Å: Chain B: C.10, E.37, D.61 Ligands: CD.8, CL.10 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:C.10, B:E.37, B:D.61, H2O.3, H2O.3

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 7 residues within 4Å: Chain A: C.10, L.19, E.37, D.61, N.65, F.66 Ligands: CD.2 Ligand excluded by PLIP CL.10: 7 residues within 4Å: Chain B: C.10, L.19, E.37, D.61, N.65, F.66 Ligands: CD.9 Ligand excluded by PLIP

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

SO4.4: 4 residues within 4Å: Chain A: K.16, R.111, H.116, L.117 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.111, A:L.117 Water bridges: A:K.118 Salt bridges: A:K.16, A:H.116 SO4.5: 5 residues within 4Å: Chain A: C.10, T.11, H.12, N.100, K.104 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:C.10, A:H.12, A:N.100 Salt bridges: A:K.104 SO4.6: 1 residues within 4Å: Chain A: R.132 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.132 SO4.11: 5 residues within 4Å: Chain B: K.16, R.111, E.115, H.116, L.117 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.115, B:L.117 Water bridges: B:K.16, B:K.118 Salt bridges: B:K.16, B:H.116 SO4.12: 4 residues within 4Å: Chain B: C.10, T.11, H.12, K.104 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.11, B:H.12 Salt bridges: B:K.104 SO4.13: 3 residues within 4Å: Chain B: G.68, A.69, T.70 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.69, B:T.70, B:T.70 Water bridges: B:G.68, B:G.68

2 x MMJ: N-methyl-1-(4-methyl-2-phenyl-1,3-thiazol-5-yl)methanamine(Non-covalent)

MMJ.7: 12 residues within 4Å: Chain A: G.51, R.52, W.53, P.54, I.149, D.152 Chain B: Y.28, N.129, H.130, G.142, E.143, V.146 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:P.54, B:Y.28 Water bridges: B:S.140 MMJ.14: 12 residues within 4Å: Chain A: Y.28, N.129, H.130, G.142, E.143, V.146 Chain B: G.51, R.52, W.53, P.54, I.149, D.152 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.28, B:P.54 Water bridges: A:S.140

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wielens, J. et al., Parallel screening of low molecular weight fragment libraries: do differences in methodology affect hit identification?. J Biomol Screen (2013)

Release Date

2013-01-30

Peptides

POL polyprotein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

POL polyprotein

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