Structure of PDB 3b6p Chain B Binding Site BS03

Receptor Information

>3b6p Chain B (length=217) Species: 10090 (Mus musculus)

GHMQTLIFLDLEATGLPSSRPEVTELCLLAVHRRALENTSISQGHPPPVP
RPPRVVDKLSLCIAPGKACSPGASEITGLSKAELEVQGRQRFDDNLAILL
RAFLQRQPQPCCLVAHNGDRYDFPLLQTELARLSTPSPLDGTFCVDSIAA
LKALEQAKSYSLGSIYTRLYWQAPTDSHTAEGDVLTLLSICQWKPQALLQ
WVDEHARPFSTVKPMYG

Ligand information

• Ligand ID: TMP
• InChI: InChI=1S/C10H15N2O8P/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(20-8)4-19-21(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1
• InChIKey: GYOZYWVXFNDGLU-XLPZGREQSA-N
• SMILES:
  CACTVS 3.341: CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O
  OpenEye OEToolkits 1.5.0: CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)O)O
  OpenEye OEToolkits 1.5.0: CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O
  CACTVS 3.341: CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O
  ACDLabs 10.04: O=C1NC(=O)N(C=C1C)C2OC(C(O)C2)COP(=O)(O)O
• Formula: C10 H15 N2 O8 P
• Name: THYMIDINE-5'-PHOSPHATE
• ChEMBL: CHEMBL394429
• DrugBank: DB01643
• ZINC: ZINC000001678872
• PDB chain: 3b6p Chain B Residue 1000

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3b6p Structural and biochemical studies of TREX1 inhibition by metals. Identification of a new active histidine conserved in DEDDh exonucleases.
• Resolution: 2.3 Å
• Binding residue (original residue number in PDB): E20 A21 L24 I84 Y129 H195
• Binding residue (residue number reindexed from 1): E12 A13 L16 I76 Y121 H178
• Annotation score: 4

Enzymatic activity

• Enzyme Commision number: 3.1.11.2: exodeoxyribonuclease III.

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0008408 3'-5' exonuclease activity

External links

• PDB: RCSB:3b6p, PDBe:3b6p, PDBj:3b6p
• PDBsum: 3b6p
• PubMed: 18780819
• UniProt: Q91XB0|TREX1_MOUSE Three-prime repair exonuclease 1 (Gene Name=Trex1)