SMTL ID : 4c0c.1

Crystal structure of Trypanosoma cruzi CYP51 bound to the inhibitor (R)-N-(3-(1H-indol-3-yl)-1-oxo-1-(pyridin-4-ylamino)propan-2-yl)-4-(4-(2,4-difluorophenyl)piperazin-1-yl)-2-fluorobenzamide.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

homo-trimer

Ligands

3 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 25 residues within 4Å: Chain A: F.70, Y.96, L.107, L.114, A.268, A.271, G.272, T.275, S.276, T.279, L.336, V.339, R.341, G.394, F.395, G.396, A.397, H.400, K.401, C.402, I.403, G.404, A.408 Ligands: WVH.2, GOL.15 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:L.114, A:A.268, A:L.336, A:F.395, A:I.403, A:I.403, A:A.408 Hydrogen bonds: A:Y.96, A:Y.96, A:A.397 Salt bridges: A:R.341 Metal complexes: A:C.402 HEM.18: 25 residues within 4Å: Chain B: F.70, Y.96, L.107, L.114, A.268, A.271, G.272, T.275, S.276, T.279, L.336, V.339, R.341, G.394, F.395, G.396, A.397, H.400, K.401, C.402, I.403, G.404, A.408 Ligands: WVH.19, GOL.32 12 PLIP interactions: 12 interactions with chain B, Hydrophobic interactions: B:L.114, B:A.268, B:L.336, B:F.395, B:I.403, B:I.403, B:A.408 Hydrogen bonds: B:Y.96, B:Y.96, B:A.397 Salt bridges: B:R.341 Metal complexes: B:C.402 HEM.35: 25 residues within 4Å: Chain C: F.70, Y.96, L.107, L.114, A.268, A.271, G.272, T.275, S.276, T.279, L.336, V.339, R.341, G.394, F.395, G.396, A.397, H.400, K.401, C.402, I.403, G.404, A.408 Ligands: WVH.36, GOL.49 12 PLIP interactions: 12 interactions with chain C, Hydrophobic interactions: C:L.114, C:A.268, C:L.336, C:F.395, C:I.403, C:I.403, C:A.408 Hydrogen bonds: C:Y.96, C:Y.96, C:A.397 Salt bridges: C:R.341 Metal complexes: C:C.402

3 x WVH: 4-[4-[2,4-bis(fluoranyl)phenyl]piperazin-1-yl]-2-fluoranyl-N-[(2R)-3-(1H-indol-3-yl)-1-oxidanylidene-1-(pyridin-4-ylamino)propan-2-yl]benzamide(Non-covalent)

WVH.2: 19 residues within 4Å: Chain A: I.25, F.28, I.50, I.52, Y.83, I.85, M.86, Y.96, F.194, F.270, A.271, T.275, L.336, M.338, M.340, M.440, V.441 Chain C: V.19 Ligands: HEM.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.28, A:Y.96, A:F.270, A:A.271, A:T.275, A:M.440 Water bridges: A:Y.83 pi-Stacking: A:Y.83, A:F.194 WVH.19: 19 residues within 4Å: Chain A: V.19 Chain B: I.25, F.28, I.50, I.52, Y.83, I.85, M.86, Y.96, F.194, F.270, A.271, T.275, L.336, M.338, M.340, M.440, V.441 Ligands: HEM.18 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.28, B:Y.96, B:F.270, B:A.271, B:T.275, B:M.440 Water bridges: B:Y.83 pi-Stacking: B:Y.83, B:F.194 WVH.36: 19 residues within 4Å: Chain B: V.19 Chain C: I.25, F.28, I.50, I.52, Y.83, I.85, M.86, Y.96, F.194, F.270, A.271, T.275, L.336, M.338, M.340, M.440, V.441 Ligands: HEM.35 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:F.28, C:Y.96, C:F.270, C:A.271, C:T.275, C:M.440 Water bridges: C:Y.83 pi-Stacking: C:Y.83, C:F.194

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

SO4.3: 5 residues within 4Å: Chain A: G.91, E.92, R.210, R.213, H.259 Ligand excluded by PLIP SO4.4: 5 residues within 4Å: Chain A: Q.120, N.121, P.124, N.311, Y.312 Ligand excluded by PLIP SO4.5: 6 residues within 4Å: Chain A: H.286, H.289, K.291, N.292, W.380, V.432 Ligand excluded by PLIP SO4.6: 3 residues within 4Å: Chain A: S.257, L.258 Ligands: SO4.12 Ligand excluded by PLIP SO4.7: 1 residues within 4Å: Chain A: D.389 Ligand excluded by PLIP SO4.8: 4 residues within 4Å: Chain A: R.327, F.392, K.401, Q.405 Ligand excluded by PLIP SO4.9: 2 residues within 4Å: Chain A: Q.27, R.38 Ligand excluded by PLIP SO4.10: 3 residues within 4Å: Chain A: G.165, E.166, R.169 Ligand excluded by PLIP SO4.11: 3 residues within 4Å: Chain A: N.173, R.175, H.176 Ligand excluded by PLIP SO4.12: 3 residues within 4Å: Chain A: S.257, H.259 Ligands: SO4.6 Ligand excluded by PLIP SO4.13: 5 residues within 4Å: Chain A: R.332, D.333, H.369, P.435, Y.437 Ligand excluded by PLIP SO4.14: 4 residues within 4Å: Chain A: P.202, L.203, S.206, A.207 Ligand excluded by PLIP SO4.17: 6 residues within 4Å: Chain A: H.438 Chain C: Y.15, H.24, Q.27, F.35, R.38 Ligand excluded by PLIP SO4.20: 5 residues within 4Å: Chain B: G.91, E.92, R.210, R.213, H.259 Ligand excluded by PLIP SO4.21: 5 residues within 4Å: Chain B: Q.120, N.121, P.124, N.311, Y.312 Ligand excluded by PLIP SO4.22: 6 residues within 4Å: Chain B: H.286, H.289, K.291, N.292, W.380, V.432 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain B: S.257, L.258 Ligands: SO4.29 Ligand excluded by PLIP SO4.24: 1 residues within 4Å: Chain B: D.389 Ligand excluded by PLIP SO4.25: 4 residues within 4Å: Chain B: R.327, F.392, K.401, Q.405 Ligand excluded by PLIP SO4.26: 2 residues within 4Å: Chain B: Q.27, R.38 Ligand excluded by PLIP SO4.27: 3 residues within 4Å: Chain B: G.165, E.166, R.169 Ligand excluded by PLIP SO4.28: 3 residues within 4Å: Chain B: N.173, R.175, H.176 Ligand excluded by PLIP SO4.29: 3 residues within 4Å: Chain B: S.257, H.259 Ligands: SO4.23 Ligand excluded by PLIP SO4.30: 5 residues within 4Å: Chain B: R.332, D.333, H.369, P.435, Y.437 Ligand excluded by PLIP SO4.31: 4 residues within 4Å: Chain B: P.202, L.203, S.206, A.207 Ligand excluded by PLIP SO4.34: 6 residues within 4Å: Chain A: Y.15, H.24, Q.27, F.35, R.38 Chain B: H.438 Ligand excluded by PLIP SO4.37: 5 residues within 4Å: Chain C: G.91, E.92, R.210, R.213, H.259 Ligand excluded by PLIP SO4.38: 5 residues within 4Å: Chain C: Q.120, N.121, P.124, N.311, Y.312 Ligand excluded by PLIP SO4.39: 6 residues within 4Å: Chain C: H.286, H.289, K.291, N.292, W.380, V.432 Ligand excluded by PLIP SO4.40: 3 residues within 4Å: Chain C: S.257, L.258 Ligands: SO4.46 Ligand excluded by PLIP SO4.41: 1 residues within 4Å: Chain C: D.389 Ligand excluded by PLIP SO4.42: 4 residues within 4Å: Chain C: R.327, F.392, K.401, Q.405 Ligand excluded by PLIP SO4.43: 2 residues within 4Å: Chain C: Q.27, R.38 Ligand excluded by PLIP SO4.44: 3 residues within 4Å: Chain C: G.165, E.166, R.169 Ligand excluded by PLIP SO4.45: 3 residues within 4Å: Chain C: N.173, R.175, H.176 Ligand excluded by PLIP SO4.46: 3 residues within 4Å: Chain C: S.257, H.259 Ligands: SO4.40 Ligand excluded by PLIP SO4.47: 5 residues within 4Å: Chain C: R.332, D.333, H.369, P.435, Y.437 Ligand excluded by PLIP SO4.48: 4 residues within 4Å: Chain C: P.202, L.203, S.206, A.207 Ligand excluded by PLIP SO4.51: 6 residues within 4Å: Chain B: Y.15, H.24, Q.27, F.35, R.38 Chain C: H.438 Ligand excluded by PLIP

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.15: 9 residues within 4Å: Chain A: I.155, A.159, A.268, M.269, G.272, Q.273, F.407, Q.411 Ligands: HEM.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.272, A:Q.273, A:Q.411 GOL.16: 5 residues within 4Å: Chain A: R.73, N.74, E.75, Y.100, H.400 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.73, A:N.74, A:N.74, A:E.75 GOL.32: 9 residues within 4Å: Chain B: I.155, A.159, A.268, M.269, G.272, Q.273, F.407, Q.411 Ligands: HEM.18 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.272, B:Q.273, B:Q.411 GOL.33: 5 residues within 4Å: Chain B: R.73, N.74, E.75, Y.100, H.400 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.73, B:N.74, B:N.74, B:E.75 GOL.49: 9 residues within 4Å: Chain C: I.155, A.159, A.268, M.269, G.272, Q.273, F.407, Q.411 Ligands: HEM.35 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.272, C:Q.273, C:Q.411 GOL.50: 5 residues within 4Å: Chain C: R.73, N.74, E.75, Y.100, H.400 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.73, C:N.74, C:N.74, C:E.75

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Calvet, C.M. et al., 4-Aminopyridyl-Based Cyp51 Inhibitors as Anti-Trypanosoma Cruzi Drug Leads with Improved Pharmacokinetic Profile and in Vivo Potency. J.Med.Chem. (2014)

Release Date

2014-08-20

Peptides

STEROL 14-ALPHA DEMETHYLASE: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

STEROL 14-ALPHA DEMETHYLASE

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