Structure of PDB 6hcw Chain A Binding Site BS02

Receptor Information
>6hcw Chain A (length=501) Species: 353152 (Cryptosporidium parvum Iowa II) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SHYTDNRYKMMECIKDAGRPFYPHKFKISMSLPAYALKYGNVENGYIDKD
TTLSLSGRVTSIRSSSSKLIFYDIFCEEQKVQIIANIMEHDISTGEFSVS
HSEIRRGDVVGFTGFPGKSKRGELSLFSKSVVLLSPCYHMLPTAISGLKD
QEVRYRQRYLDLMLNEESRKVFKLRSRAIKYIRNYFDRLGFLEVETPMLN
MIYGGAAARPFITYHNELETQLYMRIAPELYLKQLIVGGLDKVYEIGKNF
RNEGIDLTHNPEFTAMEFYMAYADYYDLMDLTEELISGLVLEIHGSLKIP
YHPDGPEGKCIEIDFTTPWKRFSFVEEIESGLGEKLKRPLDSQENIDFMV
EMCEKHEIELPHPRTAAKLLDKLAGHFVETKCTNPSFIIDHPQTMSPLAK
WHREKPEMTERFELFVLGKELCNAYTELNEPLQQRKFFEQQADAKASGDV
EACPIDETFCLALEHGLPPTGGWGLGIDRLIMFLADKNNIKEVILFPAMR
N
Ligand information
Ligand IDFYB
InChIInChI=1S/C17H16F3NO4/c18-10-1-2-13-11(7-10)12(22)8-14(25-13)15(23)21-9-16(24)3-5-17(19,20)6-4-16/h1-2,7-8,24H,3-6,9H2,(H,21,23)
InChIKeyPJBRCGHQNUWERQ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385OC1(CCC(F)(F)CC1)CNC(=O)C2=CC(=O)c3cc(F)ccc3O2
ACDLabs 12.01C1C(F)(CCC(C1)(CNC(C=2Oc3ccc(F)cc3C(C=2)=O)=O)O)F
OpenEye OEToolkits 1.7.6c1cc2c(cc1F)C(=O)C=C(O2)C(=O)NCC3(CCC(CC3)(F)F)O
FormulaC17 H16 F3 N O4
Name~{N}-[[4,4-bis(fluoranyl)-1-oxidanyl-cyclohexyl]methyl]-6-fluoranyl-4-oxidanylidene-chromene-2-carboxamide
ChEMBLCHEMBL3989220
DrugBank
ZINC
PDB chain6hcw Chain A Residue 602 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6hcw Lysyl-tRNA synthetase as a drug target in malaria and cryptosporidiosis.
Resolution1.46 Å
Binding residue
(original residue number in PDB)		R295 E297 H303 N304 F307 E464 L465 G518 L519 G520 R523
Binding residue
(residue number reindexed from 1)		R251 E253 H259 N260 F263 E420 L421 G474 L475 G476 R479
Annotation score1
Binding affinityMOAD: ic50=0.13uM
PDBbind-CN: -logKd/Ki=6.89,IC50=0.13uM
Enzymatic activity
Catalytic site (original residue number in PDB) R295 E297 T302 H303 E464 N467 R523
Catalytic site (residue number reindexed from 1) R251 E253 T258 H259 E420 N423 R479
Enzyme Commision number 6.1.1.6: lysine--tRNA ligase.
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0000166 nucleotide binding
GO:0003676 nucleic acid binding
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004824 lysine-tRNA ligase activity
GO:0005524 ATP binding
Biological Process
GO:0006418 tRNA aminoacylation for protein translation
GO:0006430 lysyl-tRNA aminoacylation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0016020 membrane

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6hcw, PDBe:6hcw, PDBj:6hcw
PDBsum6hcw
PubMed30894487
UniProtQ5CR27

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