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Structure of PDB 5qqp Chain A Binding Site BS01

Receptor Information
>5qqp Chain A (length=238) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IVGGTASVRGEWPWQVTLHTTSPTQRHLCGGSIIGNQWILTAAHCFYGVE
SPKILRVYSGILNQSEIKEDTSFFGVQEIIIHDQYKMAESGYDIALLKLE
TTVGYGDSQRPICLPSKGDRNVIYTDCWVTGWGYRKLRDKIQNTLQKAKI
PLVTNEECQKRYRGHKITHKMICAGYREGGKDACKGDSGGPLSCKHNEVW
HLVGITSWGEGCAQRERPGVYTNVVEYVDWILEKTQAV
Ligand information
Ligand IDNR7
InChIInChI=1S/C29H30ClN5O4/c1-39-29(38)32-21-10-11-22-23(16-21)33-26(36)9-4-2-3-8-25(28-31-17-24(22)34-28)35-13-12-19(15-27(35)37)18-6-5-7-20(30)14-18/h2-3,5-7,10-11,14,16-17,19,25H,4,8-9,12-13,15H2,1H3,(H,31,34)(H,32,38)(H,33,36)/b3-2+/t19-,25-/m0/s1
InChIKeyYMEHWISYYMKMFO-WOMRJYOTSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6COC(=O)Nc1ccc-2c(c1)NC(=O)CCC=CCC(c3[nH]cc2n3)N4CCC(CC4=O)c5cccc(c5)Cl
CACTVS 3.385COC(=O)Nc1ccc2c(NC(=O)CCC=CC[CH](N3CC[CH](CC3=O)c4cccc(Cl)c4)c5[nH]cc2n5)c1
OpenEye OEToolkits 2.0.6COC(=O)Nc1ccc-2c(c1)NC(=O)CC/C=C/C[C@@H](c3[nH]cc2n3)N4CC[C@@H](CC4=O)c5cccc(c5)Cl
CACTVS 3.385COC(=O)Nc1ccc2c(NC(=O)CC/C=C/C[C@H](N3CC[C@@H](CC3=O)c4cccc(Cl)c4)c5[nH]cc2n5)c1
ACDLabs 12.01c1c(cc2c(c1)c5cnc(C(CC=CCCC(N2)=O)N4C(CC(c3cccc(Cl)c3)CC4)=O)n5)NC(OC)=O
FormulaC29 H30 Cl N5 O4
Namemethyl [(5E,8S)-8-[(4S)-4-(3-chlorophenyl)-2-oxopiperidin-1-yl]-2-oxo-1,3,4,7,8,10-hexahydro-2H-12,9-(azeno)-1,10-benzodiazacyclotetradecin-15-yl]carbamate
ChEMBLCHEMBL4438562
DrugBank
ZINCZINC000205444408
PDB chain5qqp 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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PDB5qqp Structure based design of macrocyclic factor XIa inhibitors: Discovery of cyclic P1 linker moieties with improved oral bioavailability.
Resolution2.08 Å
Binding residue
(original residue number in PDB)		R39 H40 L41 H57 I151 D189 A190 C191 K192 G193 S195 T213 W215 G226 V227 Y228
Binding residue
(residue number reindexed from 1)		R26 H27 L28 H44 I141 D182 A183 C184 K185 G186 S188 T206 W208 G219 V220 Y221
Annotation score1
Binding affinityMOAD: Ki=5.3nM
PDBbind-CN: -logKd/Ki=8.28,Ki=5.3nM
BindingDB: Ki=5.3nM
Enzymatic activity
Catalytic site (original residue number in PDB) H57 D102 K192 G193 D194 S195 G196
Catalytic site (residue number reindexed from 1) H44 D93 K185 G186 D187 S188 G189
Enzyme Commision number 3.4.21.27: coagulation factor XIa.
Gene Ontology
Molecular Function
GO:0004252 serine-type endopeptidase activity
Biological Process
GO:0006508 proteolysis

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:5qqp, PDBe:5qqp, PDBj:5qqp
PDBsum5qqp
PubMed31445854
UniProtP03951|FA11_HUMAN Coagulation factor XI (Gene Name=F11)

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