SMTL ID : 7t09.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

hetero-1-1-mer

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: N.158, Y.159, H.160 Chain B: R.317 Ligands: EDO.3, FPP.26 Ligand excluded by PLIP EDO.2: 4 residues within 4Å: Chain A: Y.123, Q.124 Ligands: XMV.25, EDO.27 Ligand excluded by PLIP EDO.3: 5 residues within 4Å: Chain A: K.121, W.126, N.158, H.160 Ligands: EDO.1 Ligand excluded by PLIP EDO.4: 7 residues within 4Å: Chain A: Q.37, Y.49, Y.53, K.54, M.57, R.61 Chain B: D.85 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: R.211, E.218, S.223, L.224, E.227 Ligand excluded by PLIP EDO.6: 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.7: 7 residues within 4Å: Chain A: L.194, R.195, G.198, S.234, L.237, I.238 Chain B: R.22 Ligand excluded by PLIP EDO.8: 11 residues within 4Å: Chain A: M.335, R.336, A.337, G.338, Y.339 Chain B: F.5, T.6, P.373, I.374, F.375, N.376 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: S.173, I.178, W.183, G.216 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: P.156, M.193, V.196, D.197, N.200 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain A: K.103, S.104 Ligands: EDO.18 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain A: H.240, V.242, V.301, P.302, L.303 Ligands: EDO.13 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain A: V.242, P.302, L.303, R.336 Chain B: L.303 Ligands: EDO.12 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain A: L.109, D.140, P.141, S.143, E.144 Ligands: EDO.15 Ligand excluded by PLIP EDO.15: 7 residues within 4Å: Chain A: L.109, N.113, R.129, S.143, E.144, Y.147 Ligands: EDO.14 Ligand excluded by PLIP EDO.16: 7 residues within 4Å: Chain A: D.140, V.142, R.177, I.178, S.179, Q.182 Ligands: EDO.20 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain A: R.26, W.29, E.75, I.79 Ligand excluded by PLIP EDO.18: 3 residues within 4Å: Chain A: L.101, K.103 Ligands: EDO.11 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain A: H.149, G.150, L.153, W.189, M.193 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain A: V.142, A.181, Q.182, S.185 Ligands: EDO.16 Ligand excluded by PLIP EDO.27: 8 residues within 4Å: Chain A: Y.88 Chain B: A.86, S.87, W.90, H.139, L.141, P.142 Ligands: EDO.2 Ligand excluded by PLIP EDO.28: 6 residues within 4Å: Chain A: Y.123, Y.159, H.160 Chain B: D.195, C.236, Y.269 Ligand excluded by PLIP EDO.29: 8 residues within 4Å: Chain B: D.210, I.211, I.212, W.457, R.467, I.470, Y.516 Ligands: EDO.34 Ligand excluded by PLIP EDO.30: 6 residues within 4Å: Chain A: H.127, L.130 Chain B: R.181, E.193, V.194 Ligands: EDO.50 Ligand excluded by PLIP EDO.31: 5 residues within 4Å: Chain B: A.166, A.167, R.169, Q.170, P.446 Ligand excluded by PLIP EDO.32: 3 residues within 4Å: Chain B: A.226, C.258, R.259 Ligand excluded by PLIP EDO.33: 4 residues within 4Å: Chain B: A.105, K.111, R.507 Ligands: EDO.45 Ligand excluded by PLIP EDO.34: 8 residues within 4Å: Chain B: D.210, I.212, A.447, V.448, R.463, R.467 Ligands: EDO.29, EDO.39 Ligand excluded by PLIP EDO.35: 5 residues within 4Å: Chain B: Y.58, G.60, L.61 Ligands: 3FX.22, 3FX.23 Ligand excluded by PLIP EDO.36: 5 residues within 4Å: Chain B: P.335, I.420, H.423, K.424, M.425 Ligand excluded by PLIP EDO.37: 7 residues within 4Å: Chain B: M.425, W.477, T.496, T.497, T.498, G.505 Ligands: EDO.43 Ligand excluded by PLIP EDO.38: 4 residues within 4Å: Chain B: K.125, P.138, F.175, R.178 Ligand excluded by PLIP EDO.39: 6 residues within 4Å: Chain B: A.447, V.448, G.456, W.457, R.463 Ligands: EDO.34 Ligand excluded by PLIP EDO.40: 4 residues within 4Å: Chain B: W.162, L.506, R.507, P.510 Ligand excluded by PLIP EDO.41: 2 residues within 4Å: Chain B: P.16, A.31 Ligand excluded by PLIP EDO.42: 5 residues within 4Å: Chain B: V.9, S.14, S.38, F.41, P.308 Ligand excluded by PLIP EDO.43: 4 residues within 4Å: Chain B: R.493, N.495, T.496 Ligands: EDO.37 Ligand excluded by PLIP EDO.44: 3 residues within 4Å: Chain B: G.488, G.489 Ligands: 3FX.22 Ligand excluded by PLIP EDO.45: 5 residues within 4Å: Chain B: L.106, D.107, Q.108, K.111 Ligands: EDO.33 Ligand excluded by PLIP EDO.46: 4 residues within 4Å: Chain B: D.440, K.443, Q.518, E.519 Ligand excluded by PLIP EDO.47: 4 residues within 4Å: Chain B: S.442, K.443, G.444, C.517 Ligand excluded by PLIP EDO.48: 4 residues within 4Å: Chain B: S.430, S.433, S.434, L.437 Ligand excluded by PLIP EDO.49: 9 residues within 4Å: Chain B: A.441, S.442, K.443, G.444, L.445, E.460, R.463, Q.464, R.467 Ligand excluded by PLIP EDO.50: 5 residues within 4Å: Chain A: L.130, A.163, Y.164 Chain B: M.262 Ligands: EDO.30 Ligand excluded by PLIP EDO.51: 6 residues within 4Å: Chain B: R.178, C.179, K.180, R.181, V.187, F.251 Ligand excluded by PLIP EDO.52: 3 residues within 4Å: Chain B: S.433, R.436, L.437 Ligand excluded by PLIP EDO.53: 4 residues within 4Å: Chain B: M.177, K.180, R.181, P.182 Ligand excluded by PLIP

1 x ZN: ZINC ION(Non-covalent)

ZN.21: 5 residues within 4Å: Chain B: D.323, C.325, Y.409, H.410 Ligands: XMV.25 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.22: 6 residues within 4Å: Chain B: Y.58, G.489, K.490, D.491 Ligands: EDO.35, EDO.44 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.490, B:D.491, B:D.491, B:D.491 Water bridges: B:Y.58 3FX.23: 5 residues within 4Å: Chain B: R.62, K.63, Q.64, E.65 Ligands: EDO.35 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.62, B:Q.64, B:E.65 Water bridges: B:K.63, B:K.63, B:E.65 3FX.24: 9 residues within 4Å: Chain A: A.64 Chain B: S.123, P.124, K.125, A.133, N.134, S.135, Q.136, I.137 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:A.64, B:I.137 Hydrogen bonds: B:K.125 Salt bridges: B:K.125

1 x XMV: 4-{[5-({(2S)-2-butyl-5-oxo-4-[3-(trifluoromethoxy)phenyl]piperazin-1-yl}methyl)-1H-imidazol-1-yl]methyl}benzonitrile(Non-covalent)

XMV.25: 16 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, W.329, D.407, Y.409, H.410 Ligands: EDO.2, ZN.21, FPP.26 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.84, B:D.407, B:Y.409, A:Y.123 Hydrogen bonds: B:R.197, A:Y.123 Water bridges: B:Y.326 pi-Stacking: B:W.90, B:W.94, B:Y.409

1 x FPP: FARNESYL DIPHOSPHATE(Non-covalent)

FPP.26: 17 residues within 4Å: Chain A: Y.123, Y.159, H.160 Chain B: L.141, 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, XMV.25 19 PLIP interactions: 18 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.141, B:Y.200, B:Y.269, B:W.329, B:W.329, B:W.329, A:Y.159 Hydrogen bonds: B:Y.326 Water bridges: B:K.320, B:K.320, B:L.321, 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

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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