Structure of PDB 6ybk Chain A Binding Site BS03

Receptor Information
>6ybk Chain A (length=515) Species: 9606,83333 [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQV
AATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYN
GKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFN
LQEPYFTWPLIAADGGYAFKYAKYDIKDVGVDNAGAKAGLTFLVDLIKNK
HMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSAVNYGVTVLPTFKG
QPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAV
ALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAAS
GRQTVDEALKDAQTGSELYRQSLEIISRYLREQATGAADTAPMGASGATS
RKALETLRRVGDGVQRNHETAFQGMLRKLDIKNEDDVKSLSRVMIHVFSD
GVTNWGRIVTLISFGAFVAKHLKTINQESCIEPLAESITDVLVRTKRDWL
VKQRGWDGFVEFFHV
Ligand information
Ligand IDOK2
InChIInChI=1S/C40H38ClFN6O5S/c1-25-30(11-12-32(36(25)41)51-20-19-48-17-15-47(2)16-18-48)34-35-38(45-24-46-39(35)54-37(34)26-7-9-28(42)10-8-26)53-33(40(49)50)21-27-5-3-4-6-31(27)52-23-29-22-43-13-14-44-29/h3-14,22,24,33H,15-21,23H2,1-2H3,(H,49,50)/t33-/m1/s1
InChIKeySADZXBZFMGZHNM-MGBGTMOVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7Cc1c(ccc(c1Cl)OCCN2CCN(CC2)C)c3c4c(ncnc4sc3c5ccc(cc5)F)O[C@H](Cc6ccccc6OCc7cnccn7)C(=O)O
CACTVS 3.385CN1CCN(CCOc2ccc(c(C)c2Cl)c3c(sc4ncnc(O[CH](Cc5ccccc5OCc6cnccn6)C(O)=O)c34)c7ccc(F)cc7)CC1
OpenEye OEToolkits 2.0.7Cc1c(ccc(c1Cl)OCCN2CCN(CC2)C)c3c4c(ncnc4sc3c5ccc(cc5)F)OC(Cc6ccccc6OCc7cnccn7)C(=O)O
CACTVS 3.385CN1CCN(CCOc2ccc(c(C)c2Cl)c3c(sc4ncnc(O[C@H](Cc5ccccc5OCc6cnccn6)C(O)=O)c34)c7ccc(F)cc7)CC1
FormulaC40 H38 Cl F N6 O5 S
Name(2~{R})-2-[5-[3-chloranyl-2-methyl-4-[2-(4-methylpiperazin-1-yl)ethoxy]phenyl]-6-(4-fluorophenyl)thieno[2,3-d]pyrimidin-4-yl]oxy-3-[2-(pyrazin-2-ylmethoxy)phenyl]propanoic acid
ChEMBLCHEMBL4758300
DrugBank
ZINC
PDB chain6ybk Chain A Residue 403 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6ybk Discovery of S64315, a Potent and Selective Mcl-1 Inhibitor.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		H224 A227 F228 M231 V249 M250 V253 F254 G262 R263 T266 F270
Binding residue
(residue number reindexed from 1)		H418 A421 F422 M425 V443 M444 V447 F448 G456 R457 T460 F464
Annotation score1
Binding affinityMOAD: Ki=5nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0015144 carbohydrate transmembrane transporter activity
GO:1901982 maltose binding
Biological Process
GO:0006974 DNA damage response
GO:0008643 carbohydrate transport
GO:0015768 maltose transport
GO:0034219 carbohydrate transmembrane transport
GO:0034289 detection of maltose stimulus
GO:0042956 maltodextrin transmembrane transport
GO:0042981 regulation of apoptotic process
GO:0055085 transmembrane transport
GO:0060326 cell chemotaxis
Cellular Component
GO:0016020 membrane
GO:0030288 outer membrane-bounded periplasmic space
GO:0042597 periplasmic space
GO:0043190 ATP-binding cassette (ABC) transporter complex
GO:0055052 ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing
GO:1990060 maltose transport complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6ybk, PDBe:6ybk, PDBj:6ybk
PDBsum6ybk
PubMed33146521
UniProtP0AEX9|MALE_ECOLI Maltose/maltodextrin-binding periplasmic protein (Gene Name=malE);
Q07820|MCL1_HUMAN Induced myeloid leukemia cell differentiation protein Mcl-1 (Gene Name=MCL1)

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