SMTL ID : 3vq8.1

HIV-1 IN core domain in complex with (3R)-3,4-dihydro-2H-chromen-3-ylmethanol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 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.7: 4 residues within 4Å: Chain B: C.10, H.12, E.37 Ligands: CD.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.10, B:H.12, B:E.37 CD.8: 5 residues within 4Å: Chain B: C.10, E.37, D.61 Ligands: CD.7, CL.9 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:C.10, B:E.37, B:D.61, H2O.2, H2O.2

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.9: 7 residues within 4Å: Chain B: C.10, L.19, E.37, D.61, N.65, F.66 Ligands: CD.8 Ligand excluded by PLIP

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

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

2 x BCU: (3R)-3,4-dihydro-2H-chromen-3-ylmethanol(Non-covalent)

BCU.6: 9 residues within 4Å: Chain A: Q.40, A.43, Y.44, L.47, T.70, A.73, A.74 Chain B: Q.113, T.119 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:A.43, A:L.47, A:T.70, A:A.74, B:T.119 BCU.12: 7 residues within 4Å: Chain A: T.119 Chain B: A.43, Y.44, L.47, T.70, A.73, A.74 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:A.43, B:T.70, B:A.74, A:T.119

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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