SMTL ID : 6dwd.1

SAMHD1 Bound to Clofarabine-TP in the Catalytic Pocket and Allosteric Pocket

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

8 x HDV: 9-{2-deoxy-2-fluoro-5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}-2-me thyl-9H-purin-6-amine(Non-covalent)

HDV.1: 18 residues within 4Å: Chain A: Q.73, L.74, 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.5, MG.6 27 PLIP interactions: 27 interactions with chain A Hydrogen bonds: A:Q.73, A:R.88, A:Q.299 Water bridges: A:R.130, A:R.130, A:R.130, A:R.130, A:R.130, A:H.139, A:H.139, A:H.139, A:R.144, A:E.158, A:Y.239, A:R.290, A:R.290, A:Q.299, 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 HDV.3: 21 residues within 4Å: Chain A: D.254, 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, G.248, I.249, R.296, H.300, K.301, V.302 Ligands: MG.17, GTP.31 24 PLIP interactions: 6 interactions with chain C, 16 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: C:I.249 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:R.257, A:R.257, A:R.257, A:K.278, A:K.447 pi-Cation interactions: A:R.257, A:R.257 HDV.15: 18 residues within 4Å: Chain B: Q.73, L.74, 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.20, MG.21 25 PLIP interactions: 25 interactions with chain B Hydrogen bonds: B:Q.73, B:R.88, B:Y.239, B:Q.299 Water bridges: B:R.130, B:R.130, B:R.130, B:H.139, B:D.235, B:D.235, B:Y.239, B:R.290, B:R.290, B:Y.298, B:Q.299, B:D.307 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 HDV.18: 18 residues within 4Å: Chain A: V.41, I.42, N.43, H.49 Chain B: D.254, R.257, R.276, K.278, N.282, K.447 Chain D: V.80, F.81, G.248, I.249, R.296, H.300 Ligands: GTP.4, MG.19 30 PLIP interactions: 3 interactions with chain A, 8 interactions with chain D, 19 interactions with chain B Hydrogen bonds: A:N.43, A:N.43, B:R.257, B:N.282, B:N.282 Water bridges: A:K.40, D:H.300, D:K.301, D:K.301, B:R.257, B:R.257, B:R.257, B:R.257, B:R.276, B:K.278, B:K.278, B:K.447 Hydrophobic interactions: D:I.249 Salt bridges: D:H.300, D:H.300, D:K.301, D:K.301, B:R.257, B:R.276, B:K.278, B:K.278, B:K.278, B:K.447 pi-Cation interactions: B:R.257, B:R.257 HDV.29: 21 residues within 4Å: Chain A: V.80, F.81, G.248, I.249, R.296, H.300, K.301, V.302 Chain C: D.254, 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.39 28 PLIP interactions: 17 interactions with chain C, 8 interactions with chain A, 3 interactions with chain D Hydrogen bonds: C:R.257, C:N.282, C:N.282, D:N.43, D:N.43 Water bridges: C:R.257, C:R.257, C:R.276, C:K.278, C:K.278, C:K.447, A:K.301, A:K.301, D:K.40 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:I.249 HDV.30: 17 residues within 4Å: Chain C: Q.73, L.74, 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.32 31 PLIP interactions: 31 interactions with chain C Hydrogen bonds: C:Q.73, C:R.88, C:N.131, C:Y.239, C:Q.299 Water bridges: C:R.130, C:R.130, C:R.130, C:R.144, C:D.233, C:D.235, C:D.235, C:K.236, C:Y.239, C:R.290, C:R.290, C:Y.298, C:Q.299, C:D.307, 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, C:H.294 HDV.40: 22 residues within 4Å: Chain B: V.80, F.81, G.248, I.249, R.296, H.300, K.301, V.302 Chain C: V.41, I.42, N.43, H.49 Chain D: D.254, R.257, F.261, R.276, K.278, N.282, K.447 Ligands: GTP.16, MG.41, NA.46 28 PLIP interactions: 19 interactions with chain D, 7 interactions with chain B, 2 interactions with chain C Hydrogen bonds: D:R.257, D:N.282, B:R.296, C:N.43, C:N.43 Water bridges: D:R.257, D:R.257, D:R.257, D:R.257, D:R.276, D:K.447, D:K.447, D:K.447, D:K.447 Salt bridges: D:R.257, D:R.276, D:K.278, D:K.278, D:K.278, D:K.447, B:H.300, B:H.300, B:K.301, B:K.301, B:K.301 pi-Cation interactions: D:R.257, D:R.257 Hydrophobic interactions: B:I.249 HDV.42: 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.43 32 PLIP interactions: 32 interactions with chain D Hydrogen bonds: D:Q.73, D:R.88, D:Y.239, D:Q.299 Water bridges: D:G.77, D:R.88, D:R.130, D:R.130, D:R.130, D:R.130, D:R.130, D:R.130, D:H.139, D:H.139, D:R.144, D:R.144, D:R.290, D:R.290, D:R.290, D:Q.299, D:Q.299, D:Q.299, D:D.307 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: HDV.29, MG.39 25 PLIP interactions: 10 interactions with chain D, 9 interactions with chain A, 6 interactions with chain C Hydrogen bonds: D:V.41, D:Q.66, D:R.69, A:R.375 Water bridges: D:K.40, D:D.61, D:Q.66, A:K.301, A:K.379, A:K.379, A:Y.380, C:K.447, C:K.447, C:K.447, C:K.447 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.4: 15 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 Ligands: HDV.18, MG.19 28 PLIP interactions: 8 interactions with chain D, 14 interactions with chain A, 6 interactions with chain B Hydrogen bonds: D:R.375, A:V.41, A:Q.66, A:R.69 Water bridges: D:K.301, D:K.301, D:K.379, A:K.40, A:K.40, A:K.40, A:K.40, A:K.40, A:D.61, A:Q.66, B:K.447, B:K.447, B:K.447, B:K.447 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 GTP.16: 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: HDV.40, MG.41 23 PLIP interactions: 6 interactions with chain B, 12 interactions with chain C, 5 interactions with chain D Hydrogen bonds: B:R.375, C:V.41, C:Q.66, C:R.69 Water bridges: B:K.379, C:K.40, C:K.40, C:K.40, C:K.40, C:D.61, D:K.447, D:K.447, D:K.447 Salt bridges: B:R.375, B:K.379, B:K.379, C:K.40, C:K.40, C:K.40, C:D.61, D:K.447, D:K.447 pi-Cation interactions: B:R.375 GTP.31: 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: HDV.3, MG.17 24 PLIP interactions: 11 interactions with chain B, 9 interactions with chain C, 4 interactions with chain A Hydrogen bonds: B:V.41, B:Q.66, B:R.69, C:R.375 Water bridges: B:K.40, B:K.40, B:K.40, B:K.40, C:K.301, C:K.301, C:K.379, C:K.379, A:K.447, A:K.447 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

10 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 2 residues within 4Å: Chain A: K.236 Ligands: HDV.1 No protein-ligand interaction detected (PLIP) MG.6: 6 residues within 4Å: Chain A: R.88, H.91, R.130, N.131, D.235 Ligands: HDV.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.91, A:D.235, A:D.235 MG.17: 4 residues within 4Å: Chain A: K.447 Chain B: K.40 Ligands: HDV.3, GTP.31 No protein-ligand interaction detected (PLIP) MG.19: 4 residues within 4Å: Chain A: K.40 Chain B: K.447 Ligands: GTP.4, HDV.18 No protein-ligand interaction detected (PLIP) MG.20: 3 residues within 4Å: Chain B: D.233, K.236 Ligands: HDV.15 No protein-ligand interaction detected (PLIP) MG.21: 6 residues within 4Å: Chain B: R.88, H.91, R.130, N.131, D.235 Ligands: HDV.15 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.91, B:D.235, B:D.235 MG.32: 2 residues within 4Å: Chain C: K.236 Ligands: HDV.30 No protein-ligand interaction detected (PLIP) MG.39: 3 residues within 4Å: Chain D: K.40 Ligands: GTP.2, HDV.29 No protein-ligand interaction detected (PLIP) MG.41: 4 residues within 4Å: Chain C: K.40 Chain D: K.447 Ligands: GTP.16, HDV.40 No protein-ligand interaction detected (PLIP) MG.43: 3 residues within 4Å: Chain D: D.233, K.236 Ligands: HDV.42 No protein-ligand interaction detected (PLIP)

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

NA.7: 4 residues within 4Å: Chain A: R.257, F.258, F.261, E.279 Ligand excluded by PLIP NA.8: 4 residues within 4Å: Chain A: G.281, N.282, D.285 Chain C: R.296 Ligand excluded by PLIP NA.9: 4 residues within 4Å: Chain A: Y.380, V.381, G.382, D.507 Ligand excluded by PLIP NA.10: 7 residues within 4Å: Chain A: K.391, I.392, K.393, R.394, Y.397, N.428, Q.472 Ligand excluded by PLIP NA.11: 3 residues within 4Å: Chain A: Q.371 Ligands: NA.12, SIN.14 Ligand excluded by PLIP NA.12: 2 residues within 4Å: Ligands: NA.11, SIN.14 Ligand excluded by PLIP NA.22: 3 residues within 4Å: Chain B: F.258, E.279, N.282 Ligand excluded by PLIP NA.23: 4 residues within 4Å: Chain B: G.281, N.282, D.285 Chain D: R.296 Ligand excluded by PLIP NA.24: 4 residues within 4Å: Chain B: P.63, S.171, N.172 Chain C: Y.374 Ligand excluded by PLIP NA.25: 2 residues within 4Å: Chain B: W.209, E.216 Ligand excluded by PLIP NA.33: 3 residues within 4Å: Chain C: Q.195, Y.222, S.226 Ligand excluded by PLIP NA.34: 3 residues within 4Å: Chain B: N.349, L.352 Chain C: N.349 Ligand excluded by PLIP NA.35: 4 residues within 4Å: Chain A: H.288 Chain C: Y.284, D.285, L.465 Ligand excluded by PLIP NA.36: 2 residues within 4Å: Chain A: K.301 Chain C: K.278 Ligand excluded by PLIP NA.44: 3 residues within 4Å: Chain D: Q.195, Y.222, S.226 Ligand excluded by PLIP NA.45: 3 residues within 4Å: Chain A: N.349, L.352 Chain D: N.349 Ligand excluded by PLIP NA.46: 5 residues within 4Å: Chain B: G.248, I.249 Chain C: N.43 Chain D: D.254 Ligands: HDV.40 Ligand excluded by PLIP NA.47: 4 residues within 4Å: Chain D: P.185, E.186, I.189, C.190 Ligand excluded by PLIP NA.48: 1 residues within 4Å: Chain D: A.149 Ligand excluded by PLIP NA.49: 5 residues within 4Å: Chain A: Y.356 Chain D: N.349, I.350, E.353 Ligands: NA.51 Ligand excluded by PLIP NA.50: 2 residues within 4Å: Chain D: A.326, E.341 Ligand excluded by PLIP NA.51: 5 residues within 4Å: Chain D: I.321, E.322, I.323, E.353 Ligands: NA.49 Ligand excluded by PLIP NA.52: 3 residues within 4Å: Chain D: R.118, E.187 Ligands: TCE.56 Ligand excluded by PLIP

7 x GLY: GLYCINE(Non-covalent)

GLY.13: 3 residues within 4Å: Chain A: R.229, H.441, R.455 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.441 Salt bridges: A:R.229, A:R.272, A:H.441, A:R.455 GLY.26: 3 residues within 4Å: Chain B: Q.371, N.376, F.378 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.376 GLY.27: 3 residues within 4Å: Chain B: Q.371, Y.374, N.376 5 PLIP interactions: 2 Ligand-Ligand interactions, 3 interactions with chain B Hydrogen bonds: G.27, G.27, B:Q.371, B:Q.371, B:N.376 GLY.37: 5 residues within 4Å: Chain A: R.295, R.296 Chain C: G.281, N.282, D.285 6 PLIP interactions: 3 interactions with chain C, 2 Ligand-Ligand interactions, 1 interactions with chain A Water bridges: C:G.281, C:G.281, C:D.285 Hydrogen bonds: G.37, G.37 Salt bridges: A:R.296 GLY.53: 6 residues within 4Å: Chain B: S.292, R.295, R.296 Chain D: G.281, N.282, D.285 7 PLIP interactions: 1 Ligand-Ligand interactions, 1 interactions with chain B, 5 interactions with chain D Hydrogen bonds: G.53, B:R.296, D:G.281, D:N.282 Water bridges: D:G.281, D:G.281, D:G.281 GLY.54: 1 residues within 4Å: Chain D: K.212 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.211, D:K.212 Water bridges: D:K.212 GLY.55: 6 residues within 4Å: Chain D: S.116, R.118, D.119, R.214, K.218 Ligands: TCE.56 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:S.116 Water bridges: D:R.118, D:R.214, D:K.218, D:K.218, D:K.218 Salt bridges: D:R.118, D:R.214, D:K.218

2 x SIN: SUCCINIC ACID(Non-covalent)

SIN.14: 6 residues within 4Å: Chain A: Q.371, N.376, F.378, K.479 Ligands: NA.11, NA.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.376 Water bridges: A:V.481 SIN.38: 6 residues within 4Å: Chain C: I.368, Q.371, N.376, F.378, K.479, V.481 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:Q.371, C:F.378 Hydrogen bonds: C:N.376, C:K.479

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

PO4.28: 4 residues within 4Å: Chain B: R.229, R.272, H.441, R.455 4 PLIP interactions: 4 interactions with chain B Salt bridges: B:R.229, B:R.272, B:H.441, B:R.455

1 x TCE: 3,3',3''-phosphanetriyltripropanoic acid(Non-covalent)

TCE.56: 4 residues within 4Å: Chain D: P.215, N.217 Ligands: NA.52, GLY.55 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Ligand interactions Hydrogen bonds: D:E.187, D:N.217, G.55

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
D

B
C

C
B

D
A

Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

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