Structure of PDB 6ncf Chain B Binding Site BS02

Receptor Information
>6ncf Chain B (length=676) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SSHHHHHSYTVTVATGSQEHAGTDDYIYLSLVGSAGCSEKHLLDKGSFER
GAVDSYDVTVDEELGEIQLVRIEKRKYGSNDDWYLKYITLKTPHGDYIEF
PCYRWITGDVEVVLRDGRAKLARDDQIHILKQHRRKELETRQKQYRWMEW
NPGFPLSIDAKCHKDLPRDIQFDSEKGVDFVLNYSKAMENLFINRFMHMF
QSSWNDFADFEKIFVKISNTISERVMNHWQEDLMFGYQFLNGANPVLIRR
CTELPEKLPVTTEMVECSLERQLSLEQEVQQGNIFIVDFELLDGIDANKT
DPCTLQFLAAPICLLYKNLANKIVPIAIQLNQIPGDENPIFLPSDAKYDW
LLAKIWVRSSDFHVHQTITHLLRTHLVSEVFGIAMYRQLPAVHPIFKLLV
AHVRFTIAINTKAREQLICECGLFDKANATGGGGHVQMVQRAMKDLTYAS
LCFPEAIKARGMESKEDIPYYFYRDDGLLVWEAIRTFTAEVVDIYYEGDQ
VVEEDPELQDFVNDVYVYGMRGRKSSGFPKSVKSREQLSEYLTVVIFTAS
AQHAAVNFGQYDWASWIPNAPPTMRAPPPTAKGVVTIEQIVDTLPDRGRS
CWHLGAVWALSQFQENELFLGMYPEEHFIEKPVKEAMARFRKNLEAIVSV
IAERNENLQLPYYYLSPDRIPNSVAI
Ligand information
Ligand IDAF7
InChIInChI=1S/C32H48O5/c1-18-9-12-28(4)15-16-30(6)21(25(28)19(18)2)17-22(34)26-29(5)13-11-24(37-20(3)33)32(8,27(35)36)23(29)10-14-31(26,30)7/h17-19,23-26H,9-16H2,1-8H3,(H,35,36)/t18-,19+,23-,24-,25+,26-,28-,29+,30-,31-,32-/m1/s1
InChIKeyHMMGKOVEOFBCAU-BCDBGHSCSA-N
SMILES
SoftwareSMILES
CACTVS 3.385C[C@@H]1CC[C@]2(C)CC[C@]3(C)C(=CC(=O)[C@@H]4[C@@]5(C)CC[C@@H](OC(C)=O)[C@@](C)([C@@H]5CC[C@@]34C)C(O)=O)[C@@H]2[C@H]1C
OpenEye OEToolkits 2.0.6CC1CCC2(CCC3(C(=CC(=O)C4C3(CCC5C4(CCC(C5(C)C(=O)O)OC(=O)C)C)C)C2C1C)C)C
CACTVS 3.385C[CH]1CC[C]2(C)CC[C]3(C)C(=CC(=O)[CH]4[C]5(C)CC[CH](OC(C)=O)[C](C)([CH]5CC[C]34C)C(O)=O)[CH]2[CH]1C
OpenEye OEToolkits 2.0.6C[C@@H]1CC[C@@]2(CC[C@@]3(C(=CC(=O)[C@H]4[C@]3(CC[C@@H]5[C@@]4(CC[C@H]([C@]5(C)C(=O)O)OC(=O)C)C)C)[C@@H]2[C@H]1C)C)C
ACDLabs 12.01C45C(C3C(C=C2C1C(C)C(CCC1(C)CCC2(C)C3(C)CC4)C)=O)(C)CCC(C5(C)C(O)=O)OC(=O)C
FormulaC32 H48 O5
Name(3alpha,8alpha,17alpha,18alpha)-3-(acetyloxy)-11-oxours-12-en-23-oic acid
ChEMBLCHEMBL237111
DrugBank
ZINCZINC000014089767
PDB chain6ncf Chain B Residue 702 [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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PDB6ncf Structural and mechanistic insights into 5-lipoxygenase inhibition by natural products.
Resolution2.871 Å
Binding residue
(original residue number in PDB)		L66 R68 R101 E108 V109 V110 H130 E134 T137 R138
Binding residue
(residue number reindexed from 1)		L69 R71 R104 E111 V112 V113 H133 E137 T140 R141
Annotation score1
Binding affinityBindingDB: IC50=35600nM
Enzymatic activity
Catalytic site (original residue number in PDB) H367 H372 H550 N554 I673
Catalytic site (residue number reindexed from 1) H370 H375 H553 N557 I676
Enzyme Commision number 1.13.11.-
1.13.11.34: arachidonate 5-lipoxygenase.
Gene Ontology
Molecular Function
GO:0004051 arachidonate 5-lipoxygenase activity
GO:0004052 arachidonate 12(S)-lipoxygenase activity
GO:0005506 iron ion binding
GO:0005515 protein binding
GO:0016702 oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
GO:0016787 hydrolase activity
GO:0036403 arachidonate 8(S)-lipoxygenase activity
GO:0046872 metal ion binding
GO:0051213 dioxygenase activity
Biological Process
GO:0001676 long-chain fatty acid metabolic process
GO:0001937 negative regulation of endothelial cell proliferation
GO:0002232 leukocyte chemotaxis involved in inflammatory response
GO:0002523 leukocyte migration involved in inflammatory response
GO:0002540 leukotriene production involved in inflammatory response
GO:0006629 lipid metabolic process
GO:0006690 icosanoid metabolic process
GO:0006691 leukotriene metabolic process
GO:0006954 inflammatory response
GO:0006959 humoral immune response
GO:0016525 negative regulation of angiogenesis
GO:0019369 arachidonate metabolic process
GO:0019370 leukotriene biosynthetic process
GO:0019372 lipoxygenase pathway
GO:0030501 positive regulation of bone mineralization
GO:0034440 lipid oxidation
GO:0036336 dendritic cell migration
GO:0042593 glucose homeostasis
GO:0042759 long-chain fatty acid biosynthetic process
GO:0045598 regulation of fat cell differentiation
GO:0050727 regulation of inflammatory response
GO:0050728 negative regulation of inflammatory response
GO:0050796 regulation of insulin secretion
GO:0061044 negative regulation of vascular wound healing
GO:0061045 negative regulation of wound healing
GO:0106014 regulation of inflammatory response to wounding
GO:1900015 regulation of cytokine production involved in inflammatory response
GO:1900407 regulation of cellular response to oxidative stress
GO:1901753 leukotriene A4 biosynthetic process
GO:1903426 regulation of reactive oxygen species biosynthetic process
GO:1903573 negative regulation of response to endoplasmic reticulum stress
GO:1903671 negative regulation of sprouting angiogenesis
GO:1904999 positive regulation of leukocyte adhesion to arterial endothelial cell
GO:2001301 lipoxin biosynthetic process
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005634 nucleus
GO:0005635 nuclear envelope
GO:0005641 nuclear envelope lumen
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0016020 membrane
GO:0016363 nuclear matrix
GO:0031965 nuclear membrane
GO:0034774 secretory granule lumen
GO:0048471 perinuclear region of cytoplasm
GO:1904813 ficolin-1-rich granule lumen

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6ncf, PDBe:6ncf, PDBj:6ncf
PDBsum6ncf
PubMed32393899
UniProtP09917|LOX5_HUMAN Polyunsaturated fatty acid 5-lipoxygenase (Gene Name=ALOX5)

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