SMTL ID : 9n0v.2 (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: 25 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, K.182, N.183 18 PLIP interactions: 15 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:N.53, A:L.56, A:L.56, A:Q.63, A:L.69, A:K.70, A:K.70, A:I.73, A:I.73, A:A.105, B:Y.169 Hydrogen bonds: A:N.57, A:K.70, A:N.74, A:N.74, B:K.182 Halogen bonds: A:Q.67 pi-Cation interactions: B:K.182 01.2: 23 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 E: P.38, S.41, Y.169, L.172, R.173, Q.179, K.182 20 PLIP interactions: 2 interactions with chain E, 18 interactions with chain B Halogen bonds: E:Y.169, E:R.173, B:K.70, B:T.107 Hydrophobic interactions: B:N.53, B:L.56, B:L.56, B:M.66, B:M.66, B:L.69, B:K.70, B:K.70, B:I.73 Hydrogen bonds: B:N.57, B:N.57, B:K.70, B:N.74 pi-Cation interactions: B:K.70, B:K.70, B:K.70 01.3: 25 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, K.182, N.183 18 PLIP interactions: 15 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:N.53, C:L.56, C:L.56, C:Q.63, C:L.69, C:K.70, C:K.70, C:I.73, C:I.73, C:A.105, D:Y.169 Hydrogen bonds: C:N.57, C:K.70, C:N.74, C:N.74, D:K.182 Halogen bonds: C:Q.67 pi-Cation interactions: D:K.182 01.4: 23 residues within 4Å: Chain A: P.38, S.41, Y.169, L.172, R.173, Q.179, K.182 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 20 PLIP interactions: 2 interactions with chain A, 18 interactions with chain D Halogen bonds: A:Y.169, A:R.173, D:K.70, D:T.107 Hydrophobic interactions: D:N.53, D:L.56, D:L.56, D:M.66, D:M.66, D:L.69, D:K.70, D:K.70, D:I.73 Hydrogen bonds: D:N.57, D:N.57, D:K.70, D:N.74 pi-Cation interactions: D:K.70, D:K.70, D:K.70 01.5: 25 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, K.182, N.183 18 PLIP interactions: 15 interactions with chain E, 3 interactions with chain F Hydrophobic interactions: E:N.53, E:L.56, E:L.56, E:Q.63, E:L.69, E:K.70, E:K.70, E:I.73, E:I.73, E:A.105, F:Y.169 Hydrogen bonds: E:N.57, E:K.70, E:N.74, E:N.74, F:K.182 Halogen bonds: E:Q.67 pi-Cation interactions: F:K.182 01.6: 23 residues within 4Å: Chain C: 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: 18 interactions with chain F, 2 interactions with chain C Hydrophobic interactions: F:N.53, F:L.56, F:L.56, F:M.66, F:M.66, F:L.69, F:K.70, F:K.70, F:I.73 Hydrogen bonds: F:N.57, F:N.57, F:K.70, F:N.74 pi-Cation interactions: F:K.70, F:K.70, F:K.70 Halogen bonds: F:K.70, F:T.107, C:Y.169, C:R.173

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
C

B
D

C
C

D
D

E
C

F
D

Capsid protein p24

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