SMTL ID : 7t0e.1

Cryptococcus neoformans protein farnesyltransferase in complex with FPP and inhibitor 2b

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.22 Å

Oligo State

hetero-1-1-mer

Ligands

58 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 5 residues within 4Å: Chain A: N.158, Y.159, H.160 Chain B: R.317 Ligands: FPP.58 Ligand excluded by PLIP EDO.2: 7 residues within 4Å: Chain A: Q.37, Y.49, Y.53, K.54, M.57, R.61 Ligands: EDO.17 Ligand excluded by PLIP EDO.3: 6 residues within 4Å: Chain A: H.240, V.242, V.301, P.302, L.303 Ligands: EDO.4 Ligand excluded by PLIP EDO.4: 6 residues within 4Å: Chain A: V.242, P.302, D.333, R.336 Ligands: EDO.3, EDO.35 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: N.113, S.143, E.144, Y.147 Ligands: EDO.19 Ligand excluded by PLIP EDO.6: 7 residues within 4Å: Chain A: L.130, Y.164, W.167 Chain B: C.236, M.262 Ligands: EDO.24, EDO.37 Ligand excluded by PLIP EDO.7: 7 residues within 4Å: Chain A: R.211, E.218, T.219, S.223, L.224, E.227, F.255 Ligand excluded by PLIP EDO.8: 8 residues within 4Å: Chain A: Y.88, W.91, Q.124, H.127, H.128 Chain B: C.189, G.192, E.193 Ligand excluded by PLIP EDO.9: 7 residues within 4Å: Chain A: D.39, G.40, P.41, N.42, P.43 Chain B: S.116, T.117 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain A: P.156, M.193, V.196, D.197, N.200 Ligands: EDO.20 Ligand excluded by PLIP EDO.11: 2 residues within 4Å: Chain A: K.66, E.68 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: R.211, E.218, S.223, D.226 Ligands: EDO.15 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain A: M.23, R.26, W.29, E.75, I.79 Ligands: EDO.18 Ligand excluded by PLIP EDO.14: 8 residues within 4Å: Chain A: L.194, R.195, V.196, D.197, G.198, I.238 Chain B: R.22, P.23 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain A: W.183, L.187, L.210, R.211, R.214 Ligands: EDO.12 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain A: N.113, V.117, Y.147 Ligand excluded by PLIP EDO.17: 9 residues within 4Å: Chain A: Q.37, Y.53, M.57, H.87 Chain B: D.85, P.132, S.135, Q.136 Ligands: EDO.2 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain A: R.26, R.27, S.28 Ligands: EDO.13 Ligand excluded by PLIP EDO.19: 7 residues within 4Å: Chain A: L.109, L.133, I.136, P.138, S.143, E.144 Ligands: EDO.5 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain A: W.189, E.192, M.193, V.196 Ligands: EDO.10 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain A: N.316, R.317, V.318, D.319, D.320 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain A: R.249, L.252, K.253, S.256, L.257, L.259 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain A: S.173, G.176, R.177, I.178, W.183 Ligand excluded by PLIP EDO.24: 9 residues within 4Å: Chain A: Y.123, Y.159, H.160 Chain B: V.194, D.195, C.236, Y.269 Ligands: EDO.6, EDO.37 Ligand excluded by PLIP EDO.25: 2 residues within 4Å: Chain A: E.346, C.347 Ligand excluded by PLIP EDO.26: 3 residues within 4Å: Chain A: H.171, T.174, L.175 Ligand excluded by PLIP EDO.31: 9 residues within 4Å: Chain B: D.210, I.211, I.212, W.457, A.466, R.467, I.470, Y.516 Ligands: EDO.33 Ligand excluded by PLIP EDO.32: 3 residues within 4Å: Chain B: G.103, V.104, A.105 Ligand excluded by PLIP EDO.33: 8 residues within 4Å: Chain B: D.210, I.212, A.447, V.448, W.457, R.463, R.467 Ligands: EDO.31 Ligand excluded by PLIP EDO.34: 7 residues within 4Å: Chain A: Y.88 Chain B: A.86, S.87, W.90, H.139, L.141, P.142 Ligand excluded by PLIP EDO.35: 9 residues within 4Å: Chain A: R.336 Chain B: L.303, Q.304, Q.305, G.306, E.307, E.310, R.315 Ligands: EDO.4 Ligand excluded by PLIP EDO.36: 5 residues within 4Å: Chain B: M.425, T.496, T.498, G.505 Ligands: EDO.54 Ligand excluded by PLIP EDO.37: 7 residues within 4Å: Chain A: H.127, L.130 Chain B: E.193, V.194 Ligands: EDO.6, EDO.24, EDO.61 Ligand excluded by PLIP EDO.38: 5 residues within 4Å: Chain B: P.335, I.420, H.423, K.424, M.425 Ligand excluded by PLIP EDO.39: 4 residues within 4Å: Chain A: D.38 Chain B: H.120, A.133, N.134 Ligand excluded by PLIP EDO.40: 5 residues within 4Å: Chain B: A.166, A.167, R.169, Q.170, K.449 Ligand excluded by PLIP EDO.41: 6 residues within 4Å: Chain B: V.9, S.14, S.38, F.41, P.308, I.309 Ligand excluded by PLIP EDO.42: 5 residues within 4Å: Chain B: G.456, W.457, N.459, E.460, R.463 Ligand excluded by PLIP EDO.43: 3 residues within 4Å: Chain B: S.433, R.436, L.437 Ligand excluded by PLIP EDO.44: 6 residues within 4Å: Chain B: Q.228, T.229, Y.230, G.232, D.293, A.296 Ligand excluded by PLIP EDO.45: 3 residues within 4Å: Chain B: S.428, P.429, S.430 Ligand excluded by PLIP EDO.46: 8 residues within 4Å: Chain B: A.441, S.442, K.443, G.444, R.463, Q.464, R.467 Ligands: EDO.64 Ligand excluded by PLIP EDO.47: 5 residues within 4Å: Chain B: R.178, C.179, K.180, R.181, V.187 Ligand excluded by PLIP EDO.48: 3 residues within 4Å: Chain B: Q.390, G.403, R.405 Ligand excluded by PLIP EDO.49: 2 residues within 4Å: Chain B: M.177, K.180 Ligand excluded by PLIP EDO.50: 5 residues within 4Å: Chain B: L.106, D.107, Q.108, K.111 Ligands: EDO.57 Ligand excluded by PLIP EDO.51: 3 residues within 4Å: Chain B: G.444, P.446 Ligands: EDO.64 Ligand excluded by PLIP EDO.52: 5 residues within 4Å: Chain B: P.214, H.218, L.285, F.288 Ligands: EDO.63 Ligand excluded by PLIP EDO.53: 4 residues within 4Å: Chain B: P.214, W.457, K.458, E.462 Ligand excluded by PLIP EDO.54: 7 residues within 4Å: Chain B: L.475, W.477, T.498, G.505, L.508, K.509 Ligands: EDO.36 Ligand excluded by PLIP EDO.55: 5 residues within 4Å: Chain B: Q.170, E.174, K.449, P.450, V.451 Ligand excluded by PLIP EDO.56: 4 residues within 4Å: Chain B: R.343, P.429, R.436, N.473 Ligand excluded by PLIP EDO.57: 4 residues within 4Å: Chain B: A.105, K.111, R.507 Ligands: EDO.50 Ligand excluded by PLIP EDO.60: 4 residues within 4Å: Chain B: L.321, D.400, K.401, K.404 Ligand excluded by PLIP EDO.61: 6 residues within 4Å: Chain A: H.127, L.131 Chain B: V.187, G.191, G.192 Ligands: EDO.37 Ligand excluded by PLIP EDO.62: 4 residues within 4Å: Chain B: F.69, S.72, F.81, Q.408 Ligand excluded by PLIP EDO.63: 6 residues within 4Å: Chain B: H.218, N.219, D.221, K.222, F.288 Ligands: EDO.52 Ligand excluded by PLIP EDO.64: 5 residues within 4Å: Chain B: S.442, K.443, G.444 Ligands: EDO.46, EDO.51 Ligand excluded by PLIP

1 x ZN: ZINC ION(Non-covalent)

ZN.27: 5 residues within 4Å: Chain B: D.323, C.325, Y.409, H.410 Ligands: XOA.59 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.323, B:D.323, B:C.325, B:H.410

3 x 3FX: (2R)-3-(cyclohexylamino)-2-hydroxypropane-1-sulfonic acid(Non-covalent)

3FX.28: 4 residues within 4Å: Chain B: Y.58, G.489, K.490, D.491 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.490, B:D.491, B:D.491, B:D.491 Water bridges: B:Y.58, B:N.492 3FX.29: 4 residues within 4Å: Chain B: R.62, K.63, Q.64, E.65 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.62, B:K.63, B:Q.64, B:E.65 3FX.30: 10 residues within 4Å: Chain A: A.64, T.89 Chain B: S.123, P.124, K.125, A.133, N.134, S.135, Q.136, I.137 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:A.64, A:T.89, B:I.137 Hydrogen bonds: B:K.125, B:K.125 Salt bridges: B:K.125

1 x FPP: FARNESYL DIPHOSPHATE(Non-covalent)

FPP.58: 16 residues within 4Å: Chain A: Y.123, Y.159, H.160 Chain B: R.197, Y.200, H.266, G.268, Y.269, C.272, R.317, K.320, Y.326, W.329, Y.409 Ligands: EDO.1, XOA.59 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:R.197, B:Y.200, B:W.329, B:W.329, A:Y.159, A:Y.159 Hydrogen bonds: B:Y.326 Water bridges: B:L.321, B:L.321, B:Y.326 Salt bridges: B:H.266, B:R.317, B:R.317, B:K.320, B:K.320

1 x XOA: (5S)-4-({1-[(4-bromophenyl)methyl]-1H-imidazol-5-yl}methyl)-5-butyl-1-(3-chlorophenyl)piperazin-2-one(Non-covalent)

XOA.59: 14 residues within 4Å: Chain A: Y.123 Chain B: L.84, S.87, W.90, W.94, R.197, D.323, C.325, Y.326, D.407, Y.409, H.410 Ligands: ZN.27, FPP.58 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.84, B:D.407, B:Y.409, A:Y.123 pi-Stacking: B:W.90, B:W.94, B:Y.409

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Y. et al., Structure-Guided Discovery of Potent Antifungals that Prevent Ras Signaling by Inhibiting Protein Farnesyltransferase. J.Med.Chem. (2022)

Release Date

2022-11-09

Peptides

Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha: A
Protein farnesyltransferase subunit beta: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha

Protein farnesyltransferase subunit beta

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