Structure of PDB 8hcd Chain B Binding Site BS02

Receptor Information

>8hcd Chain B (length=220) Species: 10090 (Mus musculus)

HGHMQTLIFLDLEATGLPSSRPEVTELCLLAVHRRALENTSISQGHPPPV
PRPPRVVDKLSLCIAPGKACSPGASEITGLSKAELEVQGRQRFDDNLAIL
LRAFLQRQPQPCCLVAHNGDRYDFPLLQTELARLSTPSPLDGTFCVDSIA
ALKALEQASSKSYSLGSIYTRLYWQAPTDSHTAEGDVLTLLSICQWKPQA
LLQWVDEHARPFSTVKPMYG

Ligand information

• Ligand ID: DCM
• InChI: InChI=1S/C9H14N3O7P/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(19-8)4-18-20(15,16)17/h1-2,5-6,8,13H,3-4H2,(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
• InChIKey: NCMVOABPESMRCP-SHYZEUOFSA-N
• SMILES:
  CACTVS 3.341: NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2
  CACTVS 3.341: NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2
  OpenEye OEToolkits 1.5.0: C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)O)O
  ACDLabs 10.04: O=C1N=C(N)C=CN1C2OC(C(O)C2)COP(=O)(O)O
  OpenEye OEToolkits 1.5.0: C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=O)(O)O)O
• Formula: C9 H14 N3 O7 P
• Name: 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
• ChEMBL: CHEMBL374699
• DrugBank: DB03798
• ZINC: ZINC000003861759
• PDB chain: 8hcd Chain B Residue 302

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8hcd Molecular insight into the specific enzymatic properties of TREX1 revealing the diverse functions in processing RNA and DNA/RNA hybrids.
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): E20 A21 G23 L24 I84 Y129 H195
• Binding residue (residue number reindexed from 1): E13 A14 G16 L17 I77 Y122 H181
• 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:8hcd, PDBe:8hcd, PDBj:8hcd
• PDBsum: 8hcd
• PubMed: 37870446
• UniProt: Q91XB0|TREX1_MOUSE Three-prime repair exonuclease 1 (Gene Name=Trex1)