SMTL ID : 6dwk.1

SAMHD1 Bound to Fludarabine-TP in the Catalytic Pocket

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

4 x HFD: 2-fluoro-9-{5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}-9H-purin-6-a mine(Non-covalent)

HFD.1: 16 residues within 4Å: Chain A: Q.73, L.74, G.77, R.88, R.130, H.139, H.157, K.236, Y.239, D.243, R.290, H.294, Y.298, Q.299, D.307 Ligands: MG.14 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:Q.73, A:R.88, A:H.139, A:Y.298, A:Q.299 Water bridges: A:R.130, A:R.130, A:R.144 Salt bridges: A:R.130, A:H.157, A:K.236, A:R.290, A:R.290, A:H.294 HFD.16: 18 residues within 4Å: Chain B: Q.73, L.74, G.77, R.88, R.130, N.131, H.134, H.139, H.157, D.235, K.236, Y.239, D.243, R.290, H.294, Y.298, Q.299 Ligands: MG.25 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:Q.73, B:R.88, B:N.131, B:Y.239, B:Y.239, B:Y.239, B:Y.298, B:Q.299, B:N.304 Water bridges: B:Q.73, B:G.77, B:H.86, B:R.144, B:D.307 Salt bridges: B:R.88, B:R.130, B:H.134, B:H.139, B:H.139, B:H.157, B:H.157, B:K.236, B:R.290 HFD.33: 18 residues within 4Å: Chain C: Q.73, L.74, G.77, R.88, R.130, H.139, H.157, E.158, D.235, K.236, Y.239, D.243, R.290, H.294, Y.298, Q.299, N.304 Ligands: MG.38 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:Q.73, C:R.88, C:D.235, C:Y.239, C:Y.298, C:Q.299, C:N.304 Water bridges: C:R.88 Salt bridges: C:R.130, C:H.139, C:H.139, C:H.157, C:K.236, C:R.290, C:H.294 HFD.46: 16 residues within 4Å: Chain D: Q.73, L.74, R.88, R.130, H.139, H.157, K.236, Y.239, D.243, R.290, H.294, Y.298, Q.299 Ligands: NA.50, MG.53, MG.54 19 PLIP interactions: 19 interactions with chain D Hydrogen bonds: D:Q.73, D:R.88, D:Y.298, D:Q.299, D:N.304 Water bridges: D:R.88, D:R.88, D:R.130, D:R.130, D:R.144, D:K.236 Salt bridges: D:R.130, D:H.139, D:H.139, D:H.157, D:K.236, D:R.290, D:R.290, D:H.294

4 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.2: 16 residues within 4Å: Chain A: Y.79, V.80, V.302, R.375, K.379 Chain C: K.447 Chain D: K.40, V.41, I.42, I.60, D.61, Q.66, R.69, F.89 Ligands: DTP.31, MG.44 19 PLIP interactions: 6 interactions with chain A, 11 interactions with chain D, 2 interactions with chain C Hydrogen bonds: A:R.375, D:V.41, D:Q.66, D:R.69 Salt bridges: A:K.301, A:R.375, A:K.379, A:K.379, D:K.40, D:K.40, D:K.40, D:D.61, C:K.447, C:K.447 pi-Cation interactions: A:R.375 Water bridges: D:K.40, D:K.40, D:D.61, D:Q.66 GTP.6: 16 residues within 4Å: Chain A: K.40, V.41, I.42, I.60, D.61, Q.66, R.69, F.89 Chain B: K.447 Chain D: Y.79, V.80, V.302, R.375, K.379 Ligands: MG.5, DTP.18 15 PLIP interactions: 4 interactions with chain D, 9 interactions with chain A, 2 interactions with chain B Salt bridges: D:R.375, D:K.379, D:K.379, A:K.40, A:K.40, A:K.40, A:D.61, B:K.447, B:K.447 pi-Cation interactions: D:R.375 Hydrogen bonds: A:V.41, A:Q.66, A:R.69 Water bridges: A:K.40, A:D.61 GTP.17: 17 residues within 4Å: Chain B: Y.79, V.80, V.302, R.375, L.377, K.379 Chain C: K.40, V.41, I.42, I.60, D.61, Q.66, R.69, F.89 Chain D: K.447 Ligands: MG.32, DTP.45 17 PLIP interactions: 2 interactions with chain D, 8 interactions with chain C, 7 interactions with chain B Salt bridges: D:K.447, D:K.447, C:K.40, C:K.40, C:K.40, C:D.61, B:R.375, B:K.379, B:K.379 Hydrogen bonds: C:V.41, C:Q.66, C:R.69, B:R.375 Water bridges: C:K.40, B:K.379, B:K.379 pi-Cation interactions: B:R.375 GTP.34: 17 residues within 4Å: Chain A: K.447 Chain B: K.40, V.41, I.42, I.60, D.61, Q.66, R.69, F.89 Chain C: Y.79, V.80, V.302, R.375, L.377, K.379 Ligands: DTP.3, MG.4 19 PLIP interactions: 11 interactions with chain B, 4 interactions with chain A, 4 interactions with chain C Hydrogen bonds: B:V.41, B:Q.66, B:R.69 Water bridges: B:K.40, B:K.40, B:D.61, B:Q.66, A:K.447, A:K.447 Salt bridges: B:K.40, B:K.40, B:K.40, B:D.61, A:K.447, A:K.447, C:R.375, C:K.379, C:K.379 pi-Cation interactions: C:R.375

4 x DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE(Non-covalent)

DTP.3: 19 residues within 4Å: Chain A: R.257, F.261, R.276, K.278, N.282, K.447 Chain B: V.41, I.42, N.43, H.49 Chain C: V.80, F.81, I.249, R.296, H.300, K.301, V.302 Ligands: MG.4, GTP.34 21 PLIP interactions: 7 interactions with chain C, 12 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: C:V.80, C:F.81 Salt bridges: C:H.300, C:H.300, C:K.301, C:K.301, C:K.301, A:R.257, A:R.276, A:K.278, A:K.278, A:K.278, A:K.447 Hydrogen bonds: A:R.257, A:N.282, A:N.282, B:N.43, B:N.43 Water bridges: A:K.447 pi-Cation interactions: A:R.257, A:R.257 DTP.18: 19 residues within 4Å: Chain A: V.41, I.42, N.43, H.49 Chain B: R.257, F.261, R.276, K.278, N.282, K.447 Chain D: V.80, F.81, I.249, R.296, H.300, K.301, V.302 Ligands: MG.5, GTP.6 25 PLIP interactions: 7 interactions with chain D, 16 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: D:V.80, D:F.81 Salt bridges: D:H.300, D:H.300, D:K.301, D:K.301, D:K.301, B:R.257, B:R.276, B:K.278, B:K.278, B:K.278, B:K.447 Hydrogen bonds: B:R.257, B:N.282, B:N.282, A:N.43, A:N.43 Water bridges: B:R.257, B:R.276, B:R.276, B:R.276, B:K.278 pi-Cation interactions: B:R.257, B:R.257 DTP.31: 19 residues within 4Å: Chain A: V.80, F.81, I.249, R.296, H.300, K.301, V.302 Chain C: R.257, F.261, R.276, K.278, N.282, K.447 Chain D: V.41, I.42, N.43, H.49 Ligands: GTP.2, MG.44 20 PLIP interactions: 7 interactions with chain A, 11 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: A:V.80, A:F.81 Salt bridges: A:H.300, A:H.300, A:K.301, A:K.301, A:K.301, C:R.257, C:R.276, C:K.278, C:K.278, C:K.278, C:K.447 Hydrogen bonds: C:R.257, C:N.282, C:N.282, D:N.43, D:N.43 pi-Cation interactions: C:R.257, C:R.257 DTP.45: 18 residues within 4Å: Chain B: V.80, F.81, I.249, R.296, H.300, K.301 Chain C: V.41, I.42, N.43, H.49 Chain D: R.257, F.261, R.276, K.278, N.282, K.447 Ligands: GTP.17, MG.32 20 PLIP interactions: 7 interactions with chain B, 11 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: B:V.80, B:F.81 Salt bridges: B:H.300, B:H.300, B:K.301, B:K.301, B:K.301, D:R.257, D:R.276, D:K.278, D:K.278, D:K.278, D:K.447 Hydrogen bonds: D:R.257, D:N.282, D:N.282, C:N.43, C:N.43 pi-Cation interactions: D:R.257, D:R.257

9 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: K.447 Chain B: K.40 Ligands: DTP.3, GTP.34 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain A: K.40 Ligands: GTP.6, DTP.18 No protein-ligand interaction detected (PLIP) MG.14: 5 residues within 4Å: Chain A: R.130, D.233, D.235, K.236 Ligands: HFD.1 No protein-ligand interaction detected (PLIP) MG.25: 5 residues within 4Å: Chain B: R.130, D.233, D.235, K.236 Ligands: HFD.16 No protein-ligand interaction detected (PLIP) MG.32: 3 residues within 4Å: Chain C: K.40 Ligands: GTP.17, DTP.45 No protein-ligand interaction detected (PLIP) MG.38: 4 residues within 4Å: Chain C: K.236, Y.239, R.290 Ligands: HFD.33 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:Y.239 MG.44: 3 residues within 4Å: Chain D: K.40 Ligands: GTP.2, DTP.31 No protein-ligand interaction detected (PLIP) MG.53: 2 residues within 4Å: Chain D: H.139 Ligands: HFD.46 No protein-ligand interaction detected (PLIP) MG.54: 6 residues within 4Å: Chain D: R.88, N.131, H.134, H.139, H.157 Ligands: HFD.46 No protein-ligand interaction detected (PLIP)

23 x NA: SODIUM ION(Non-functional Binders)

NA.7: 6 residues within 4Å: Chain A: P.82, G.83, S.85 Chain D: H.86, E.90, H.246 Ligand excluded by PLIP NA.8: 3 residues within 4Å: Chain A: I.372, R.375 Chain D: Q.66 Ligand excluded by PLIP NA.9: 4 residues within 4Å: Chain A: Q.195, Y.222, V.225, S.226 Ligand excluded by PLIP NA.10: 3 residues within 4Å: Chain A: H.47, Y.255, K.256 Ligand excluded by PLIP NA.11: 2 residues within 4Å: Chain A: Q.371, Y.374 Ligand excluded by PLIP NA.12: 6 residues within 4Å: Chain A: K.72, S.85, N.87 Chain D: K.72, S.85, N.87 Ligand excluded by PLIP NA.13: 5 residues within 4Å: Chain A: Y.445, C.446, A.449, R.452 Chain C: V.510 Ligand excluded by PLIP NA.19: 7 residues within 4Å: Chain B: S.92, G.127, L.128, C.129, R.130, N.131 Ligands: NA.20 Ligand excluded by PLIP NA.20: 9 residues within 4Å: Chain B: F.65, L.68, S.92, L.128, C.129, R.130, N.131, L.132 Ligands: NA.19 Ligand excluded by PLIP NA.21: 6 residues within 4Å: Chain B: P.82, G.83, S.85 Chain C: H.86, E.90, H.246 Ligand excluded by PLIP NA.22: 3 residues within 4Å: Chain B: I.372, R.375 Chain C: Q.66 Ligand excluded by PLIP NA.23: 4 residues within 4Å: Chain B: E.266, N.451, R.452, A.453 Ligand excluded by PLIP NA.24: 7 residues within 4Å: Chain B: Q.463, L.464, L.465, E.467 Chain D: P.466, E.467, K.468 Ligand excluded by PLIP NA.30: 3 residues within 4Å: Chain B: Y.79, E.373 Chain C: Y.70 Ligand excluded by PLIP NA.35: 3 residues within 4Å: Chain B: Q.66 Chain C: I.372, R.375 Ligand excluded by PLIP NA.36: 3 residues within 4Å: Chain C: H.288, N.291, Y.431 Ligand excluded by PLIP NA.37: 4 residues within 4Å: Chain C: R.276, D.277, C.446, K.447 Ligand excluded by PLIP NA.47: 4 residues within 4Å: Chain D: Q.195, Y.222, V.225, S.226 Ligand excluded by PLIP NA.48: 3 residues within 4Å: Chain A: Q.66 Chain D: I.372, R.375 Ligand excluded by PLIP NA.49: 6 residues within 4Å: Chain B: R.296 Chain D: N.252, F.253, N.282, D.285, M.286 Ligand excluded by PLIP NA.50: 5 residues within 4Å: Chain D: Y.298, G.303, N.304, D.307 Ligands: HFD.46 Ligand excluded by PLIP NA.51: 3 residues within 4Å: Chain D: V.162, E.166, K.193 Ligand excluded by PLIP NA.52: 4 residues within 4Å: Chain D: R.290, N.291, D.430 Ligands: GLY.55 Ligand excluded by PLIP

12 x GLY: GLYCINE(Non-covalent)(Non-functional Binders)

GLY.15: 6 residues within 4Å: Chain A: R.290, H.294, Q.299, N.428, M.429, D.430 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.290, A:R.290, A:Q.299, A:D.430, A:D.430 Salt bridges: A:R.290, A:H.294 GLY.26: 6 residues within 4Å: Chain B: S.116, R.118, D.119, R.214, P.215, K.218 7 PLIP interactions: 2 Ligand-Ligand interactions, 5 interactions with chain B Hydrogen bonds: G.26, G.26, B:S.116, B:R.214 Salt bridges: B:R.118, B:R.214, B:K.218 GLY.27: 4 residues within 4Å: Chain B: R.229, R.272, H.441, R.455 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.229, B:R.272, B:R.455 Salt bridges: B:R.272 GLY.39: 1 residues within 4Å: Ligands: GLY.40 2 PLIP interactions: 2 Ligand-Ligand interactions Hydrogen bonds: G.40, G.40 GLY.40: 3 residues within 4Å: Chain C: R.483, Y.487 Ligands: GLY.39 2 PLIP interactions: 2 Ligand-Ligand interactions Hydrogen bonds: G.39, G.39 GLY.41: 2 residues within 4Å: Chain C: Y.374, N.376 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Ligand interactions Hydrogen bonds: C:N.376, G.41, G.41 GLY.42: 5 residues within 4Å: Chain C: R.290, H.294, N.428, M.429, D.430 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.290, C:D.430, C:D.430, C:D.430 Salt bridges: C:R.290, C:H.294 GLY.43: 5 residues within 4Å: Chain C: S.116, R.118, D.119, R.214, K.218 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.116, C:S.116 Salt bridges: C:R.118, C:R.214, C:K.218 GLY.55: 7 residues within 4Å: Chain D: R.290, H.294, Q.299, N.428, M.429, D.430 Ligands: NA.52 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:R.290, D:R.290, D:Q.299, D:D.430, D:D.430 Salt bridges: D:H.294 GLY.56: 2 residues within 4Å: Chain D: G.248, Q.250 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.254 GLY.57: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:K.418 GLY.58: 4 residues within 4Å: Chain D: V.411, L.412, Y.487, L.514 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:L.412, D:L.412

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.28: 4 residues within 4Å: Chain B: K.363, R.366, E.367, K.370 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.366, B:E.367 TRS.29: 5 residues within 4Å: Chain B: L.412, D.414, R.483, K.484, Y.487 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.414, B:D.414, B:R.483, B:R.483, B:Y.487

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.59: 4 residues within 4Å: Chain D: R.229, R.272, H.441, R.455 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.272, D:R.455 Salt bridges: D:R.229, D:H.441

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Knecht, K.M. et al., The structural basis for cancer drug interactions with the catalytic and allosteric sites of SAMHD1. Proc. Natl. Acad. Sci. U.S.A. (2018)

Release Date

2018-10-10

Peptides

Deoxynucleoside triphosphate triphosphohydrolase SAMHD1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

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