Structure of PDB 3k23 Chain A Binding Site BS03

Receptor Information

>3k23 Chain A (length=245) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

LPQLTPTLVSLLEVIEPEVLYAGYDSVPDSTWRIMTTLNMLGGRQVIAAV
KWAKAIPGFRNLHLDDQMTLLQYSWMYLMAFALGWRSYRQSSANLLCFAP
DLIINEQGMYDQCKHMLYVSSELHRLQVSYEEYLCMKTLLLLSSVPKDGL
KSQELFDEIRMTYIKELGKAIVKREGNSSQNWQRFYQLTKLLDSMHEVVE
NLLNYCFQTFLDKMSIEFPEMLAEIITNQIPKYSNGNIKKLLFHQ

Ligand information

Ligand ID

JZN

InChI

InChI=1S/C34H37F4N5O4/c1-20-13-26(40-19-33(46,34(36,37)38)18-32(2,3)25-16-22(35)10-11-29(25)47-4)24-17-41-43(28(24)14-20)23-8-5-7-21(15-23)31(45)42-12-6-9-27(42)30(39)44/h5,7-8,10-11,13-17,27,40,46H,6,9,12,18-19H2,1-4H3,(H2,39,44)/t27-,33-/m1/s1

InChIKey

AKJCJJOQRAGWOW-ZORMNXRFSA-N

SMILES

Software	SMILES
CACTVS 3.352	COc1ccc(F)cc1C(C)(C)C[C@@](O)(CNc2cc(C)cc3n(ncc23)c4cccc(c4)C(=O)N5CCC[C@@H]5C(N)=O)C(F)(F)F
ACDLabs 11.02	Fc1cc(c(OC)cc1)C(C)(C)CC(O)(C(F)(F)F)CNc2cc(cc3c2cnn3c5cc(C(=O)N4C(C(=O)N)CCC4)ccc5)C
OpenEye OEToolkits 1.7.0	Cc1cc(c2cnn(c2c1)c3cccc(c3)C(=O)N4CCC[C@@H]4C(=O)N)NC[C@](CC(C)(C)c5cc(ccc5OC)F)(C(F)(F)F)O
OpenEye OEToolkits 1.7.0	Cc1cc(c2cnn(c2c1)c3cccc(c3)C(=O)N4CCCC4C(=O)N)NCC(CC(C)(C)c5cc(ccc5OC)F)(C(F)(F)F)O
CACTVS 3.352	COc1ccc(F)cc1C(C)(C)C[C](O)(CNc2cc(C)cc3n(ncc23)c4cccc(c4)C(=O)N5CCC[CH]5C(N)=O)C(F)(F)F

Formula

C34 H37 F4 N5 O4

Name

1-{[3-(4-{[(2R)-4-(5-fluoro-2-methoxyphenyl)-2-hydroxy-4-methyl-2-(trifluoromethyl)pentyl]amino}-6-methyl-1H-indazol-1-yl)phenyl]carbonyl}-D-prolinamide

PDB chain

3k23 Chain A Residue 1 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

Global view

Local view

Structure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

PDB	3k23 Design and x-ray crystal structures of high-potency nonsteroidal glucocorticoid agonists exploiting a novel binding site on the receptor.
Resolution	3.0 Å
Binding residue (original residue number in PDB)	P541 M560 L563 N564 L566 Q570 M601 L603 M604 A605 A607 L608 F623 C736
Binding residue (residue number reindexed from 1)	P17 M35 L38 N39 L41 Q45 M76 L78 M79 A80 A82 L83 F98 C206
Annotation score	1
Binding affinity	PDBbind-CN: -logKd/Ki=8.20,IC50=6.3nM BindingDB: IC50=6.3nM

Enzymatic activity

Enzyme Commision number

External links

PDB	RCSB:3k23, PDBe:3k23, PDBj:3k23
PDBsum	3k23
PubMed	19822747
UniProt	P04150\|GCR_HUMAN Glucocorticoid receptor (Gene Name=NR3C1)

[Back to BioLiP]