SMTL ID : 6dw3.1

SAMHD1 Bound to Cytarabine-TP in the Catalytic Pocket

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

4 x HF4: 4-amino-1-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}pyrimidin-2(1H)-one(Non-covalent)

HF4.1: 17 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 22 PLIP interactions: 22 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:H.139, A:Y.298, A:Q.299, A:Q.299, A:N.304, A:D.307 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 HF4.6: 17 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.10 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:Q.73, B:R.88, B:N.131, B:D.235, B:Y.239, B:Q.299 Water bridges: B:R.130, B:R.130, B:Y.298, B:Q.299 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 HF4.13: 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.14 22 PLIP interactions: 22 interactions with chain C Hydrophobic interactions: C:H.139 Hydrogen bonds: C:Q.73, C:R.88, C:N.131, C:Y.239, C:Q.299, C:Q.299 Water bridges: C:R.130, C:R.130, C:R.130, C:R.130, C:D.235, C:R.290, C:R.290 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 HF4.19: 17 residues within 4Å: Chain D: 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 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:H.139 Hydrogen bonds: D:Q.73, D:R.88, D:Y.298, 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

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

DTP.2: 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.7, GTP.8 22 PLIP interactions: 8 interactions with chain C, 12 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: C:V.80, C:F.81 Hydrogen bonds: C:R.296, A:R.257, A:N.282, B:N.43, B:N.43 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 Water bridges: A:R.276, A:K.278 pi-Cation interactions: A:R.257, A:R.257 DTP.9: 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.3, GTP.4 22 PLIP interactions: 7 interactions with chain D, 13 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.276, B:K.278 pi-Cation interactions: B:R.257, B:R.257 DTP.11: 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: MG.15, GTP.16 21 PLIP interactions: 12 interactions with chain C, 7 interactions with chain A, 2 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.276 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.17: 18 residues within 4Å: Chain B: V.80, F.81, 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.12, MG.18 23 PLIP interactions: 2 interactions with chain C, 15 interactions with chain D, 6 interactions with chain B Hydrogen bonds: C:N.43, C:N.43, D:R.257, D:N.282, D:N.282 Water bridges: D:R.257, D:R.257, D:K.278, D:K.278 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 pi-Cation interactions: D:R.257, D:R.257 Hydrophobic interactions: B:V.80, B:F.81

8 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: K.40 Ligands: GTP.4, DTP.9 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain A: D.233, K.236 Ligands: HF4.1 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain B: K.40 Ligands: DTP.2, GTP.8 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain B: R.130, S.226 Ligands: HF4.6 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain C: D.235, K.236 Ligands: HF4.13 No protein-ligand interaction detected (PLIP) MG.15: 4 residues within 4Å: Chain C: K.447 Chain D: K.40 Ligands: DTP.11, GTP.16 No protein-ligand interaction detected (PLIP) MG.18: 3 residues within 4Å: Chain D: K.447 Ligands: GTP.12, DTP.17 No protein-ligand interaction detected (PLIP) MG.20: 3 residues within 4Å: Chain D: D.233, K.236 Ligands: HF4.19 No protein-ligand interaction detected (PLIP)

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

GTP.4: 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.3, DTP.9 15 PLIP interactions: 5 interactions with chain D, 8 interactions with chain A, 2 interactions with chain B Hydrogen bonds: D:R.375, A:V.41, A:Q.66, A:R.69 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 Water bridges: A:K.40 GTP.8: 16 residues within 4Å: Chain A: K.447 Chain B: K.40, V.41, I.42, V.57, I.60, D.61, Q.66, R.69, F.89 Chain C: Y.79, V.80, V.302, R.375 Ligands: DTP.2, MG.7 16 PLIP interactions: 5 interactions with chain C, 9 interactions with chain B, 2 interactions with chain A Water bridges: C:R.375, B:K.40, B:Q.66 Salt bridges: C:R.375, C:K.379, C:K.379, B:K.40, B:K.40, B:K.40, B:D.61, A:K.447, A:K.447 pi-Cation interactions: C:R.375 Hydrogen bonds: B:V.41, B:Q.66, B:R.69 GTP.12: 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: DTP.17, MG.18 16 PLIP interactions: 9 interactions with chain C, 5 interactions with chain B, 2 interactions with chain D Hydrogen bonds: C:V.41, C:Q.66, C:R.69, B:R.375 Water bridges: C:K.40, C:D.61 Salt bridges: C:K.40, C:K.40, C:K.40, C:D.61, B:R.375, B:K.379, B:K.379, D:K.447, D:K.447 pi-Cation interactions: B:R.375 GTP.16: 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.11, MG.15 17 PLIP interactions: 11 interactions with chain D, 2 interactions with chain C, 4 interactions with chain A Hydrogen bonds: D:V.41, D:Q.66, D:R.69 Water bridges: D:K.40, D:K.40, D:D.61, D:Q.66 Salt bridges: D:K.40, D:K.40, D:K.40, D:D.61, C:K.447, C:K.447, A:R.375, A:K.379, A:K.379 pi-Cation interactions: A:R.375

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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