Structure of PDB 5nb7 Chain A Binding Site BS01

Receptor Information
>5nb7 Chain A (length=230) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ILGGREAEAHARPYMASVQLNGAHLCGGVLVAEQWVLSAAHCLEDAADGK
VQVLLGAHSLSQPEPSKRLYDVLRAVPHPDSQPDTIDHDLLLLQLSEKAT
LGPAVRPLPWQRVDRDVAPGTLCDVAGWGIVNHAGRRPDSLQHVLLPVLD
RATCNRRTHHDGAITERLMCAESNRRDSCKGDSGGPLVCGGVLEGVVTSG
SRVCGNRKKPGIYTRVASYAAWIDSVLASA
Ligand information
Ligand ID8NQ
InChIInChI=1S/C21H19BrN6O3/c22-16-6-3-7-17(24-16)25-21(31)15-9-11-8-14(11)28(15)18(29)10-27-13-5-2-1-4-12(13)19(26-27)20(23)30/h1-7,11,14-15H,8-10H2,(H2,23,30)(H,24,25,31)/t11-,14-,15+/m1/s1
InChIKeyCWZUTHDJLNZLCM-DFBGVHRSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1ccc2c(c1)c(nn2CC(=O)N3[C@@H]4C[C@@H]4C[C@H]3C(=O)Nc5cccc(n5)Br)C(=O)N
CACTVS 3.385NC(=O)c1nn(CC(=O)N2[C@@H]3C[C@@H]3C[C@H]2C(=O)Nc4cccc(Br)n4)c5ccccc15
CACTVS 3.385NC(=O)c1nn(CC(=O)N2[CH]3C[CH]3C[CH]2C(=O)Nc4cccc(Br)n4)c5ccccc15
OpenEye OEToolkits 2.0.6c1ccc2c(c1)c(nn2CC(=O)N3C4CC4CC3C(=O)Nc5cccc(n5)Br)C(=O)N
FormulaC21 H19 Br N6 O3
Name1-[2-[(1~{R},3~{S},5~{R})-3-[(6-bromanylpyridin-2-yl)carbamoyl]-2-azabicyclo[3.1.0]hexan-2-yl]-2-oxidanylidene-ethyl]indazole-3-carboxamide
ChEMBLCHEMBL3683753
DrugBank
ZINCZINC000143934784
PDB chain5nb7 Chain A Residue 303 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5nb7 Discovery of Highly Potent and Selective Small-Molecule Reversible Factor D Inhibitors Demonstrating Alternative Complement Pathway Inhibition in Vivo.
Resolution1.33 Å
Binding residue
(original residue number in PDB)
L41 C42 H57 C58 W141 G142 C191 K192 G193 S195 S215 G216 S217 R218
Binding residue
(residue number reindexed from 1)
L25 C26 H41 C42 W128 G129 C179 K180 G181 S183 S199 G200 S201 R202
Annotation score1
Binding affinityMOAD: ic50=0.006uM
PDBbind-CN: -logKd/Ki=8.22,IC50=0.006uM
BindingDB: IC50=9nM
Enzymatic activity
Catalytic site (original residue number in PDB) H57 D102 K192 G193 D194 S195 G196
Catalytic site (residue number reindexed from 1) H41 D89 K180 G181 D182 S183 G184
Enzyme Commision number 3.4.21.46: complement factor D.
Gene Ontology
Molecular Function
GO:0004252 serine-type endopeptidase activity
GO:0008236 serine-type peptidase activity
Biological Process
GO:0006508 proteolysis
GO:0006956 complement activation
GO:0006957 complement activation, alternative pathway
GO:0009617 response to bacterium
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0031093 platelet alpha granule lumen
GO:0034774 secretory granule lumen
GO:0070062 extracellular exosome
GO:1904813 ficolin-1-rich granule lumen

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Biological Process

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Cellular Component
External links
PDB RCSB:5nb7, PDBe:5nb7, PDBj:5nb7
PDBsum5nb7
PubMed28621538
UniProtP00746|CFAD_HUMAN Complement factor D (Gene Name=CFD)

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