Structure of PDB 6e69 Chain C Binding Site BS01

Receptor Information

>6e69 Chain C (length=218) Species: 9606 (Homo sapiens)

IVGGRRARPHAWPFMVSLQLRGGHFCGATLIAPNFVMSAAHCVANVNVRA
VRVVLGAHNLSRREPTRQVFAVQRIFENGYDPVNLLNDIVILQLNGSATI
NANVQVAQLPAQGRRLGNGVQCLAMGWGLLGRNRGIASVLQELNVTVVTS
LCRRSNVCTLVRGRQAGVCFGDSGSPLVCNGLIHGIASFVRGGCASGLYP
DAFAPVAQFVNWIDSIIQ

Ligand information

• Ligand ID: FUC
• InChI: InChI=1S/C6H12O5/c1-2-3(7)4(8)5(9)6(10)11-2/h2-10H,1H3/t2-,3+,4+,5-,6+/m0/s1
• InChIKey: SHZGCJCMOBCMKK-SXUWKVJYSA-N
• SMILES:
  CACTVS 3.341: C[C@@H]1O[C@@H](O)[C@@H](O)[C@H](O)[C@@H]1O
  ACDLabs 10.04: OC1C(O)C(OC(O)C1O)C
  OpenEye OEToolkits 1.5.0: CC1C(C(C(C(O1)O)O)O)O
  OpenEye OEToolkits 1.5.0: C[C@H]1[C@H]([C@H]([C@@H]([C@@H](O1)O)O)O)O
  CACTVS 3.341: C[CH]1O[CH](O)[CH](O)[CH](O)[CH]1O
• Formula: C6 H12 O5
• Name: alpha-L-fucopyranose;
  alpha-L-fucose;
  6-deoxy-alpha-L-galactopyranose;
  L-fucose;
  fucose
• ChEMBL: CHEMBL1232862
• DrugBank: DB04473
• ZINC: ZINC000001532814
• PDB chain: 6e69 Chain I Residue 3

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6e69 SuFEx-enabled, agnostic discovery of covalent inhibitors of human neutrophil elastase.
• Resolution: 2.33 Å
• Binding residue (original residue number in PDB): W27 Q135 V200 C201 N202
• Binding residue (residue number reindexed from 1): W12 Q121 V178 C179 N180
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): H57 D102 F192 G193 D194 S195 G196
• Catalytic site (residue number reindexed from 1): H41 D88 F170 G171 D172 S173 G174
• Enzyme Commision number: 3.4.21.37: leukocyte elastase.

Gene Ontology

Molecular Function

• GO:0002020 protease binding
• GO:0003714 transcription corepressor activity
• GO:0004175 endopeptidase activity
• GO:0004252 serine-type endopeptidase activity
• GO:0005515 protein binding
• GO:0008201 heparin binding
• GO:0008233 peptidase activity
• GO:0008236 serine-type peptidase activity
• GO:0019955 cytokine binding

Biological Process

• GO:0000122 negative regulation of transcription by RNA polymerase II
• GO:0001878 response to yeast
• GO:0002438 acute inflammatory response to antigenic stimulus
• GO:0002523 leukocyte migration involved in inflammatory response
• GO:0002812 biosynthetic process of antibacterial peptides active against Gram-negative bacteria
• GO:0006508 proteolysis
• GO:0006874 intracellular calcium ion homeostasis
• GO:0006909 phagocytosis
• GO:0009411 response to UV
• GO:0022617 extracellular matrix disassembly
• GO:0030163 protein catabolic process
• GO:0032496 response to lipopolysaccharide
• GO:0032682 negative regulation of chemokine production
• GO:0032717 negative regulation of interleukin-8 production
• GO:0032757 positive regulation of interleukin-8 production
• GO:0042742 defense response to bacterium
• GO:0043406 positive regulation of MAP kinase activity
• GO:0048661 positive regulation of smooth muscle cell proliferation
• GO:0050728 negative regulation of inflammatory response
• GO:0050778 positive regulation of immune response
• GO:0050832 defense response to fungus
• GO:0050900 leukocyte migration
• GO:0050922 negative regulation of chemotaxis
• GO:0070269 pyroptotic inflammatory response
• GO:0070945 neutrophil-mediated killing of gram-negative bacterium
• GO:0070947 neutrophil-mediated killing of fungus
• GO:1903238 positive regulation of leukocyte tethering or rolling

Cellular Component

• GO:0005576 extracellular region
• GO:0005615 extracellular space
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0009986 cell surface
• GO:0017053 transcription repressor complex
• GO:0030141 secretory granule
• GO:0031410 cytoplasmic vesicle
• GO:0035578 azurophil granule lumen
• GO:0035580 specific granule lumen
• GO:0045335 phagocytic vesicle
• GO:0062023 collagen-containing extracellular matrix
• GO:0070062 extracellular exosome

External links

• PDB: RCSB:6e69, PDBe:6e69, PDBj:6e69
• PDBsum: 6e69
• PubMed: 31484779
• UniProt: P08246|ELNE_HUMAN Neutrophil elastase (Gene Name=ELANE)