SMTL ID : 6dwj.1

SAMHD1 Bound to Vidarabine-TP in the Catalytic Pocket

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

4 x HEJ: 9-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}-9H-purin-6-amine(Non-covalent)

HEJ.1: 16 residues within 4Å: Chain A: Q.73, L.74, R.88, R.130, H.134, H.139, H.157, D.235, K.236, Y.239, D.243, R.290, H.294, Y.298, Q.299 Ligands: MG.6 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:Q.73, A:R.88, A:Q.299 Water bridges: A:R.130, A:R.130, A:D.235, A:Y.298, A:Q.299 Salt bridges: A:R.88, A:R.130, A:H.134, A:H.139, A:H.157, A:H.157, A:K.236, A:R.290 pi-Stacking: A:H.139 HEJ.12: 16 residues within 4Å: Chain B: Q.73, L.74, R.88, R.130, H.134, H.139, H.157, D.235, K.236, Y.239, D.243, R.290, H.294, Y.298, Q.299 Ligands: MG.16 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:Q.73, B:R.88, B:D.235, B:Y.239, B:Q.299 Water bridges: B:R.130, B:R.130, B:R.130, B:R.130, B:Y.239, B:R.290 Salt bridges: B:R.88, B:R.130, B:H.134, B:H.139, B:H.157, B:H.157, B:K.236, B:R.290 pi-Stacking: B:H.139 HEJ.23: 16 residues within 4Å: Chain C: Q.73, L.74, R.88, R.130, 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 19 PLIP interactions: 19 interactions with chain C Hydrogen bonds: C:Q.73, C:R.88, C:Y.239, C:Q.299 Water bridges: C:R.130, C:D.235, C:Y.298, C:Q.299, C:D.307, C:D.307 Salt bridges: C:R.88, C:R.130, C:H.134, C:H.139, C:H.157, C:H.157, C:K.236, C:R.290 pi-Stacking: C:H.139 HEJ.34: 16 residues within 4Å: Chain D: Q.73, L.74, R.88, R.130, H.134, H.139, H.157, D.235, K.236, Y.239, D.243, R.290, H.294, Y.298, Q.299 Ligands: MG.36 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:Q.73, D:R.88, D:Q.299 Water bridges: D:R.130, D:R.130 Salt bridges: D:R.88, D:R.130, D:H.134, D:H.139, D:H.157, D:H.157, D:K.236, D:R.290 pi-Stacking: D:H.139

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.21, MG.32 15 PLIP interactions: 9 interactions with chain D, 4 interactions with chain A, 2 interactions with chain C Hydrogen bonds: D:V.41, D:Q.66, D:R.69 Water bridges: D:K.40, D:K.40 Salt bridges: D:K.40, D:K.40, D:K.40, D:D.61, A:R.375, A:K.379, A:K.379, C:K.447, C:K.447 pi-Cation interactions: A:R.375 GTP.5: 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.4, DTP.15 15 PLIP interactions: 8 interactions with chain A, 5 interactions with chain D, 2 interactions with chain B Hydrogen bonds: A:V.41, A:Q.66, A:R.69 Water bridges: A:D.61 Salt bridges: A:K.40, A:K.40, A:K.40, A:D.61, D:K.301, D:R.375, D:K.379, D:K.379, B:K.447, B:K.447 pi-Cation interactions: D:R.375 GTP.13: 16 residues within 4Å: Chain B: Y.79, V.80, V.302, R.375, 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.22, DTP.33 17 PLIP interactions: 2 interactions with chain D, 10 interactions with chain C, 5 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, C:R.69, B:R.375 Water bridges: C:K.40, C:K.40 pi-Cation interactions: B:R.375 GTP.24: 16 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, K.379 Ligands: DTP.3, MG.14 14 PLIP interactions: 7 interactions with chain B, 5 interactions with chain C, 2 interactions with chain A Hydrogen bonds: B:V.41, B:Q.66, B:R.69, C:R.375 Salt bridges: B:K.40, B:K.40, B:K.40, B:D.61, C:R.375, C:K.379, C:K.379, A:K.447, A:K.447 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.14, GTP.24 20 PLIP interactions: 10 interactions with chain A, 8 interactions with chain C, 2 interactions with chain B Hydrogen bonds: A:R.257, A:N.282, C:R.296, B:N.43, B:N.43 Salt bridges: A:R.257, A:R.276, A:K.278, A:K.278, A:K.278, A:K.447, C:H.300, C:H.300, C:K.301, C:K.301, C:K.301 pi-Cation interactions: A:R.257, A:R.257 Hydrophobic interactions: C:V.80, C:F.81 DTP.15: 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.4, GTP.5 21 PLIP interactions: 7 interactions with chain D, 12 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:D.254 pi-Cation interactions: B:R.257, B:R.257 DTP.21: 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.32 21 PLIP interactions: 12 interactions with chain C, 7 interactions with chain A, 2 interactions with chain D Hydrogen bonds: C:R.257, C:R.257, C:N.282, C:N.282, D:N.43, D:N.43 Salt bridges: C:R.257, C:R.276, C:K.278, C:K.278, C:K.278, C:K.447, A:H.300, A:H.300, A:K.301, A:K.301, A:K.301 pi-Cation interactions: C:R.257, C:R.257 Hydrophobic interactions: A:V.80, A:F.81 DTP.33: 19 residues within 4Å: Chain B: V.80, F.81, I.249, R.296, H.300, K.301, V.302 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.13, MG.22 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

10 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: K.40 Ligands: GTP.5, DTP.15 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain A: D.233, K.236 Ligands: HEJ.1 No protein-ligand interaction detected (PLIP) MG.7: 5 residues within 4Å: Chain A: K.72, Q.73, L.74, A.84, H.86 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:A.84, A:H.86 MG.14: 3 residues within 4Å: Chain B: K.40 Ligands: DTP.3, GTP.24 No protein-ligand interaction detected (PLIP) MG.16: 3 residues within 4Å: Chain B: D.233, K.236 Ligands: HEJ.12 No protein-ligand interaction detected (PLIP) MG.22: 3 residues within 4Å: Chain C: K.40 Ligands: GTP.13, DTP.33 No protein-ligand interaction detected (PLIP) MG.25: 3 residues within 4Å: Chain C: D.233, K.236 Ligands: HEJ.23 No protein-ligand interaction detected (PLIP) MG.32: 4 residues within 4Å: Chain C: K.447 Chain D: K.40 Ligands: GTP.2, DTP.21 No protein-ligand interaction detected (PLIP) MG.35: 5 residues within 4Å: Chain D: K.72, Q.73, L.74, A.84, H.86 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:A.84, D:H.86 MG.36: 3 residues within 4Å: Chain D: D.233, K.236 Ligands: HEJ.34 No protein-ligand interaction detected (PLIP)

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

NA.8: 5 residues within 4Å: Chain A: H.134, G.135, S.138, F.141, D.142 Ligand excluded by PLIP NA.9: 3 residues within 4Å: Chain A: H.47, Y.255, K.256 Ligand excluded by PLIP NA.10: 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.11: 5 residues within 4Å: Chain A: D.37, T.38, P.54, V.57, R.58 Ligand excluded by PLIP NA.17: 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.18: 2 residues within 4Å: Chain B: A.241, H.245 Ligand excluded by PLIP NA.19: 6 residues within 4Å: Chain B: Y.431, G.432, M.433, Q.434, K.436, F.469 Ligand excluded by PLIP NA.20: 2 residues within 4Å: Chain B: R.290, D.430 Ligand excluded by PLIP NA.26: 2 residues within 4Å: Chain C: H.288, Y.431 Ligand excluded by PLIP NA.27: 5 residues within 4Å: Chain C: K.72, Q.73, L.74, A.84, H.86 Ligand excluded by PLIP NA.28: 3 residues within 4Å: Chain C: Y.284, Y.431, P.466 Ligand excluded by PLIP NA.29: 4 residues within 4Å: Chain C: E.223, N.227, N.230, I.273 Ligand excluded by PLIP NA.37: 7 residues within 4Å: Chain A: N.43, P.45 Chain D: F.81, P.82, G.83, H.246, L.247 Ligand excluded by PLIP NA.38: 2 residues within 4Å: Chain D: A.241, H.245 Ligand excluded by PLIP NA.39: 6 residues within 4Å: Chain A: H.86, E.90, H.246 Chain D: P.82, G.83, S.85 Ligand excluded by PLIP NA.40: 3 residues within 4Å: Chain D: H.47, Y.255, K.256 Ligand excluded by PLIP NA.41: 4 residues within 4Å: Chain B: K.504, Q.506 Chain D: R.455, Q.460 Ligand excluded by PLIP

1 x GLY: GLYCINE(Non-covalent)

GLY.30: 5 residues within 4Å: Chain A: G.281, N.282, D.285 Chain C: R.295, R.296 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:G.281 Salt bridges: C:R.295

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

PO4.31: 1 residues within 4Å: Chain C: H.441 1 PLIP interactions: 1 interactions with chain C Salt bridges: C: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

2018-10-24

Peptides

Deoxynucleoside triphosphate triphosphohydrolase SAMHD1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
C

C
B

D
A

Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

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