Structure of PDB 3iid Chain A Binding Site BS01

Receptor Information

>3iid Chain A (length=185) Species: 9606 (Homo sapiens)

ADGFTVLSTKSLFLGQKLQVVQADIASIDSDAVVHPTNTDFYIGGEVGNT
LEKKGGKEFVEAVLELRKKNGPLEVAGAAVSAGHGLPAKFVIHCNSPVWG
ADKCEELLEKTVKNCLALADDKKLKSIAFPSIGSGRNGFPKQTAAQLILK
AISSYFVSTMSSSIKTVYFVLFDSESIGIYVQEMA

Ligand information

• Ligand ID: APR
• InChI: InChI=1S/C15H23N5O14P2/c16-12-7-13(18-3-17-12)20(4-19-7)14-10(23)8(21)5(32-14)1-30-35(26,27)34-36(28,29)31-2-6-9(22)11(24)15(25)33-6/h3-6,8-11,14-15,21-25H,1-2H2,(H,26,27)(H,28,29)(H2,16,17,18)/t5-,6-,8-,9-,10-,11-,14-,15-/m1/s1
• InChIKey: SRNWOUGRCWSEMX-KEOHHSTQSA-N
• SMILES:
  ACDLabs 10.04: O=P(O)(OCC3OC(n1c2ncnc(N)c2nc1)C(O)C3O)OP(=O)(O)OCC4OC(O)C(O)C4O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)O)O)O)O)O)N
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)O)O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH](O)[CH](O)[CH]4O)[CH](O)[CH]3O
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@@H](O)[C@H](O)[C@@H]4O)[C@@H](O)[C@H]3O
• Formula: C15 H23 N5 O14 P2
• Name: ADENOSINE-5-DIPHOSPHORIBOSE
• ChEMBL: CHEMBL1231026
• ZINC: ZINC000017654550
• PDB chain: 3iid Chain A Residue 400

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3iid A macrodomain-containing histone rearranges chromatin upon sensing PARP1 activation.
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): D203 I204 P215 T216 Y221 G224 E225 V226 T229 S275 S310 G312 S313 G314 R315 N316 F351 D352
• Binding residue (residue number reindexed from 1): D24 I25 P36 T37 Y42 G45 E46 V47 T50 S96 S131 G133 S134 G135 R136 N137 F172 D173
• Annotation score: 4

External links

• PDB: RCSB:3iid, PDBe:3iid, PDBj:3iid
• PDBsum: 3iid
• PubMed: 19680243
• UniProt: O75367|H2AY_HUMAN Core histone macro-H2A.1 (Gene Name=MACROH2A1)