SMTL ID : 9n0v.1 (1 other biounit)

Crystal structure of the HIV capsid hexamer bound to the small molecule long-acting inhibitor, KFA-027

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.98 Å

Oligo State

homo-hexamer

Ligands

6 x 01: N-[(1S)-1-{(3M)-3-[4-chloro-3-(methanesulfonamido)-1-(2,2,2-trifluoroethyl)-1H-indazol-7-yl]-6-[3-(methanesulfonyl)-3-methylbut-1-yn-1-yl]pyridin-2-yl}-2-phenylethyl]-2-[(3bS,4aR)-5,5-difluoro-3-(trifluoromethyl)-3b,4,4a,5-tetrahydro-1H-cyclopropa[3,4]cyclopenta[1,2-c]pyrazol-1-yl]acetamide

01.1: 26 residues within 4Å: Chain A: Q.50, N.53, T.54, L.56, N.57, Q.63, M.66, Q.67, L.69, K.70, I.73, N.74, A.105, G.106, T.107, Y.130 Chain B: I.37, P.38, S.41, I.135, Y.169, L.172, R.173, Q.179, K.182, N.183 20 PLIP interactions: 3 interactions with chain B, 17 interactions with chain A Hydrogen bonds: B:Q.179, B:K.182, A:N.57, A:K.70, A:N.74, A:N.74 pi-Cation interactions: B:R.173, A:K.70, A:K.70 Hydrophobic interactions: A:Q.50, A:L.56, A:L.56, A:M.66, A:M.66, A:L.69, A:K.70, A:K.70, A:I.73, A:A.105 Halogen bonds: A:N.57 01.2: 24 residues within 4Å: Chain B: Q.50, N.53, T.54, L.56, N.57, Q.63, M.66, Q.67, L.69, K.70, I.73, N.74, A.105, G.106, T.107, Y.130 Chain C: I.37, P.38, S.41, Y.169, L.172, R.173, Q.179, K.182 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:Q.50, B:L.56, B:L.56, B:M.66, B:M.66, B:L.69, B:L.69, B:K.70, B:K.70, B:I.73, B:A.105, B:T.107 Hydrogen bonds: B:N.57, B:N.57, B:K.70, B:N.74, B:N.74 pi-Cation interactions: B:K.70 Halogen bonds: B:K.70, B:N.74 01.3: 26 residues within 4Å: Chain C: Q.50, N.53, T.54, L.56, N.57, Q.63, M.66, Q.67, L.69, K.70, I.73, N.74, A.105, G.106, T.107, Y.130 Chain D: I.37, P.38, S.41, I.135, Y.169, L.172, R.173, Q.179, K.182, N.183 20 PLIP interactions: 17 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:Q.50, C:L.56, C:L.56, C:M.66, C:M.66, C:L.69, C:K.70, C:K.70, C:I.73, C:A.105 Hydrogen bonds: C:N.57, C:K.70, C:N.74, C:N.74, D:Q.179, D:K.182 pi-Cation interactions: C:K.70, C:K.70, D:R.173 Halogen bonds: C:N.57 01.4: 24 residues within 4Å: Chain D: Q.50, N.53, T.54, L.56, N.57, Q.63, M.66, Q.67, L.69, K.70, I.73, N.74, A.105, G.106, T.107, Y.130 Chain E: I.37, P.38, S.41, Y.169, L.172, R.173, Q.179, K.182 20 PLIP interactions: 20 interactions with chain D Hydrophobic interactions: D:Q.50, D:L.56, D:L.56, D:M.66, D:M.66, D:L.69, D:L.69, D:K.70, D:K.70, D:I.73, D:A.105, D:T.107 Hydrogen bonds: D:N.57, D:N.57, D:K.70, D:N.74, D:N.74 pi-Cation interactions: D:K.70 Halogen bonds: D:K.70, D:N.74 01.5: 26 residues within 4Å: Chain E: Q.50, N.53, T.54, L.56, N.57, Q.63, M.66, Q.67, L.69, K.70, I.73, N.74, A.105, G.106, T.107, Y.130 Chain F: I.37, P.38, S.41, I.135, Y.169, L.172, R.173, Q.179, K.182, N.183 20 PLIP interactions: 17 interactions with chain E, 3 interactions with chain F Hydrophobic interactions: E:Q.50, E:L.56, E:L.56, E:M.66, E:M.66, E:L.69, E:K.70, E:K.70, E:I.73, E:A.105 Hydrogen bonds: E:N.57, E:K.70, E:N.74, E:N.74, F:Q.179, F:K.182 pi-Cation interactions: E:K.70, E:K.70, F:R.173 Halogen bonds: E:N.57 01.6: 24 residues within 4Å: Chain A: I.37, P.38, S.41, Y.169, L.172, R.173, Q.179, K.182 Chain F: Q.50, N.53, T.54, L.56, N.57, Q.63, M.66, Q.67, L.69, K.70, I.73, N.74, A.105, G.106, T.107, Y.130 20 PLIP interactions: 20 interactions with chain F Hydrophobic interactions: F:Q.50, F:L.56, F:L.56, F:M.66, F:M.66, F:L.69, F:L.69, F:K.70, F:K.70, F:I.73, F:A.105, F:T.107 Hydrogen bonds: F:N.57, F:N.57, F:K.70, F:N.74, F:N.74 pi-Cation interactions: F:K.70 Halogen bonds: F:K.70, F:N.74

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dinh, T.T. et al., Delineating structural functionalities of Lenacapavir amenable to modifications for targeting emerging drug-resistant HIV-1 capsid variants. To Be Published

Release Date

2025-06-18

Peptides

Capsid protein p24: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Capsid protein p24

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