Structure of PDB 7a1f Chain A Binding Site BS02

Receptor Information

>7a1f Chain A (length=329) Species: 9606 (Homo sapiens)

MNGVLIPHTPIAVDFWSLRRAGTARLFFLSHMHSDHTVGLSSTWARPLYC
SPITAHLLHRHLQVSKQWIQALEVGESHVLPLDEIGQETMTVTLLDANHC
PGSVMFLFEGYFGTILYTGDFRYTPSMLKEPALTLGKQIHTLYLDNTNCN
PALVLPSRQEAAHQIVQLIRKHPQHNIKIGLYSLGKESLLEQLALEFQTW
VVLSPRRLELVQLLGLADVFTVEEKAGRIHAVDHMEICHSNMLRWNQTHP
TIAILPTSRKIHSSHPDIHVIPYSDHSSYSELRAFVAALKPCQVVPIVSR
RPCGGFQDSLSPRISVPLIPDSVQQYMSS

Ligand information

• Ligand ID: D5M
• InChI: InChI=1S/C10H14N5O6P/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(21-7)2-20-22(17,18)19/h3-7,16H,1-2H2,(H2,11,12,13)(H2,17,18,19)/t5-,6+,7+/m0/s1
• InChIKey: KHWCHTKSEGGWEX-RRKCRQDMSA-N
• SMILES:
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(O)=O)O3
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(O)O)O)N
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO[P](O)(O)=O)O3
  ACDLabs 10.04: O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)CC3O
• Formula: C10 H14 N5 O6 P
• Name: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
• ChEMBL: CHEMBL1206239
• ZINC: ZINC000001713574
• PDB chain: 7a1f Chain A Residue 403

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7a1f A phosphate binding pocket is a key determinant of exo- versus endo-nucleolytic activity in the SNM1 nuclease family.
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): T147 Y182 T257 S258 R259 S274 D275 H276
• Binding residue (residue number reindexed from 1): T147 Y182 T257 S258 R259 S274 D275 H276
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 3.1.-.-
  3.5.2.6: beta-lactamase.

External links

• PDB: RCSB:7a1f, PDBe:7a1f, PDBj:7a1f
• PDBsum: 7a1f
• PubMed: 34387694
• UniProt: Q9H816|DCR1B_HUMAN 5' exonuclease Apollo (Gene Name=DCLRE1B)