Structure of PDB 3k23 Chain B Binding Site BS02

Receptor Information

>3k23 Chain B (length=247) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

QLTPTLVSLLEVIEPEVLYAGYDSSVPDSTWRIMTTLNMLGGRQVIAAVK
WAKAIPGFRNLHLDDQMTLLQYSWMYLMAFALGWRSYRQSSANLLCFAPD
LIINEQRMTLPGMYDQCKHMLYVSSELHRLQVSYEEYLCMKTLLLLSSVP
KDGLKSQELFDEIRMTYIKELGKAIVKRESQNWQRFYQLTKLLDSMHEVV
ENLLNYCFQTFLDKTMSIEFPEMLAEIITNQIPKYSNGNIKKLLFHQ

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 B Residue 2 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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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 M604 A607 R611 F623 Q642 M646 L732 Y735
Binding residue (residue number reindexed from 1)	P15 M34 L37 N38 L40 Q44 M78 A81 R85 F97 Q116 M120 L203 Y206
Annotation score	1
Binding affinity	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)

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