Structure of PDB 5fck Chain A Binding Site BS01

Receptor Information
>5fck Chain A (length=225) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ILGGREAEAHARPYMASVQLNGAHLCGGVLVAEQWVLSAAHCLDGKVQVL
LGAHSLSQPEPSKRLYDVLRAVPHPDSQPDTIDHDLLLLQLSEKATLGPA
VRPLPWQRVDRDVAPGTLCDVAGWGIVNHAGRRPDSLQHVLLPVLDRATC
NRRTHHDGAITERLMCAESNRRDSCKGDSGGPLVCGGVLEGVVTSGSRVC
GNRKKPGIYTRVASYAAWIDSVLAS
Ligand information
Ligand ID5WC
InChIInChI=1S/C23H22ClFN6O3/c1-11(13-3-2-4-15(24)20(13)25)28-23(34)17-8-12-7-16(12)31(17)19(32)10-30-18-9-27-6-5-14(18)21(29-30)22(26)33/h2-6,9,11-12,16-17H,7-8,10H2,1H3,(H2,26,33)(H,28,34)/t11-,12-,16-,17+/m1/s1
InChIKeyYAALCKJNOOFODD-SKNMWMDOSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.4CC(c1cccc(c1F)Cl)NC(=O)C2CC3CC3N2C(=O)Cn4c5cnccc5c(n4)C(=O)N
OpenEye OEToolkits 2.0.4C[C@H](c1cccc(c1F)Cl)NC(=O)[C@@H]2C[C@H]3C[C@H]3N2C(=O)Cn4c5cnccc5c(n4)C(=O)N
CACTVS 3.385C[CH](NC(=O)[CH]1C[CH]2C[CH]2N1C(=O)Cn3nc(C(N)=O)c4ccncc34)c5cccc(Cl)c5F
CACTVS 3.385C[C@@H](NC(=O)[C@@H]1C[C@H]2C[C@H]2N1C(=O)Cn3nc(C(N)=O)c4ccncc34)c5cccc(Cl)c5F
FormulaC23 H22 Cl F N6 O3
Name1-[2-[(1~{R},3~{S},5~{R})-3-[[(1~{R})-1-(3-chloranyl-2-fluoranyl-phenyl)ethyl]carbamoyl]-2-azabicyclo[3.1.0]hexan-2-yl]-2-oxidanylidene-ethyl]pyrazolo[3,4-c]pyridine-3-carboxamide
ChEMBLCHEMBL3678914
DrugBank
ZINCZINC000143957115
PDB chain5fck Chain A Residue 301 [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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PDB5fck Small-molecule factor D inhibitors targeting the alternative complement pathway.
Resolution1.86 Å
Binding residue
(original residue number in PDB)		H40 L41 C42 H57 C58 R151 C191 K192 G193 S195 S215 G216 S217 R218 C220
Binding residue
(residue number reindexed from 1)		H24 L25 C26 H41 C42 R133 C175 K176 G177 S179 S195 G196 S197 R198 C200
Annotation score1
Binding affinityMOAD: Kd=0.006uM
PDBbind-CN: -logKd/Ki=8.22,Kd=0.006uM
BindingDB: IC50=10nM
Enzymatic activity
Catalytic site (original residue number in PDB) H57 D102 K192 G193 D194 S195 G196
Catalytic site (residue number reindexed from 1) H41 D85 K176 G177 D178 S179 G180
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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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5fck, PDBe:5fck, PDBj:5fck
PDBsum5fck
PubMed27775713
UniProtP00746|CFAD_HUMAN Complement factor D (Gene Name=CFD)

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