Structure of PDB 8vkz Chain A Binding Site BS02

Receptor Information
>8vkz Chain A (length=240) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TPTLVSLLEVIEPEVLYAGYDSSVPDSTWRIMTTLNMLGGRQMIAAVKWA
KAIPGFRNLHLDDQMTLLQYSWMSLMAFALGWRSYRQSSANLLCFAPDLI
INEQRPDMYDQCKHMLYVSSELHRLQVSYEEYLCMKTLLLLSSVPKDGLK
SQELFDEIRMTYIKELGKAIVSQNWQRFYQLTKLLDSMHEVVENLLNYCF
QTFLDKTMSIEFPEMLAEIITNQIPKYSNGNIKKLLFHQK
Ligand information
Ligand IDA1ACE
InChIInChI=1S/C35H39NO6/c1-33-13-12-25(38)16-23(33)10-11-26-27-17-30-35(29(40)19-37,34(27,2)18-28(39)31(26)33)42-32(41-30)22-8-6-20(7-9-22)14-21-4-3-5-24(36)15-21/h3-9,12-13,15-16,26-28,30-32,37,39H,10-11,14,17-19,36H2,1-2H3/t26-,27-,28+,30+,31+,32+,33-,34-,35+/m0/s1
InChIKeyMPEPSOPXQDGEHP-XSZYCUJUSA-N
SMILES
SoftwareSMILES
CACTVS 3.385C[C@]12C[C@H](O)[C@H]3[C@@H](CCC4=CC(=O)C=C[C@]34C)[C@@H]1C[C@H]5O[C@H](O[C@@]25C(=O)CO)c6ccc(Cc7cccc(N)c7)cc6
CACTVS 3.385C[C]12C[CH](O)[CH]3[CH](CCC4=CC(=O)C=C[C]34C)[CH]1C[CH]5O[CH](O[C]25C(=O)CO)c6ccc(Cc7cccc(N)c7)cc6
OpenEye OEToolkits 2.0.7CC12CC(C3C(C1CC4C2(OC(O4)c5ccc(cc5)Cc6cccc(c6)N)C(=O)CO)CCC7=CC(=O)C=CC37C)O
OpenEye OEToolkits 2.0.7C[C@]12C[C@@H]([C@H]3[C@H]([C@@H]1C[C@@H]4[C@]2(O[C@@H](O4)c5ccc(cc5)Cc6cccc(c6)N)C(=O)CO)CCC7=CC(=O)C=C[C@]37C)O
ACDLabs 12.01Nc1cccc(c1)Cc1ccc(cc1)C1OC2CC3C4CCC5=CC(=O)C=CC5(C)C4C(O)CC3(C)C2(O1)C(=O)CO
FormulaC35 H39 N O6
Name(4aR,4bS,5R,6aS,6bS,8R,9aR,10aR,10bR)-8-{4-[(3-aminophenyl)methyl]phenyl}-5-hydroxy-6b-(hydroxyacetyl)-4a,6a-dimethyl-4a,4b,5,6,6a,6b,9a,10,10a,10b,11,12-dodecahydro-2H,8H-naphtho[2',1':4,5]indeno[1,2-d][1,3]dioxol-2-one
ChEMBL
DrugBank
ZINC
PDB chain8vkz Chain A Residue 901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8vkz Minimising the payload solvent exposed hydrophobic surface area optimises the antibody-drug conjugate properties
Resolution2.133 Å
Binding residue
(original residue number in PDB)
L563 N564 Q570 M601 M604 F623 M639 C643 M646 Y735 C736 T739
Binding residue
(residue number reindexed from 1)
L35 N36 Q42 M73 M76 F95 M108 C112 M115 Y198 C199 T202
Annotation score1
Enzymatic activity
Enzyme Commision number ?
External links
PDB RCSB:8vkz, PDBe:8vkz, PDBj:8vkz
PDBsum8vkz
PubMed38516584
UniProtP04150|GCR_HUMAN Glucocorticoid receptor (Gene Name=NR3C1)

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