Structure of PDB 6d4a Chain A Binding Site BS01

Receptor Information
>6d4a Chain A (length=123) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NFWLQVQESVTVQEGLCVLVPCTFFHPIPYYDKNSPVHGYWFREGAIISR
DSPVATNKLDQEVQEETQGRFRLLGDPSRNNCSLSIVDARRRDNGSYFFR
MERGSTKYSYKSPQLSVHVTDLT
Ligand information
Ligand IDFVP
InChIInChI=1S/C42H64N6O20/c1-18-10-21(11-19(2)29(18)53)38(60)44-13-24(51)30(54)37-28(45-27(52)15-48-14-22(46-47-48)20-6-4-3-5-7-20)23(50)12-42(68-37,41(61)62)64-17-26-31(55)32(56)34(58)40(66-26)67-36-25(16-49)65-39(63-9-8-43)35(59)33(36)57/h10-11,14,20,23-26,28,30-37,39-40,49-51,53-59H,3-9,12-13,15-17,43H2,1-2H3,(H,44,60)(H,45,52)(H,61,62)/t23-,24+,25+,26+,28+,30+,31-,32-,33+,34+,35+,36+,37+,39+,40-,42+/m0/s1
InChIKeyDQZXNLDRAKHEEK-XCGJJDHASA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6Cc1cc(cc(c1O)C)C(=O)NCC(C(C2C(C(CC(O2)(C(=O)O)OCC3C(C(C(C(O3)OC4C(OC(C(C4O)O)OCCN)CO)O)O)O)O)NC(=O)Cn5cc(nn5)C6CCCCC6)O)O
CACTVS 3.385Cc1cc(cc(C)c1O)C(=O)NC[CH](O)[CH](O)[CH]2O[C](C[CH](O)[CH]2NC(=O)Cn3cc(nn3)C4CCCCC4)(OC[CH]5O[CH](O[CH]6[CH](O)[CH](O)[CH](OCCN)O[CH]6CO)[CH](O)[CH](O)[CH]5O)C(O)=O
ACDLabs 12.01C6CCCC(c5cn(CC(NC2C(C(C(O)CNC(c1cc(c(c(c1)C)O)C)=O)O)OC(CC2O)(C(O)=O)OCC3C(C(C(C(O3)OC4C(O)C(C(OC4CO)OCCN)O)O)O)O)=O)nn5)C6
OpenEye OEToolkits 2.0.6Cc1cc(cc(c1O)C)C(=O)NC[C@H]([C@H]([C@H]2[C@@H]([C@H](C[C@@](O2)(C(=O)O)OC[C@@H]3[C@@H]([C@@H]([C@H]([C@@H](O3)O[C@@H]4[C@H](O[C@H]([C@@H]([C@H]4O)O)OCCN)CO)O)O)O)O)NC(=O)Cn5cc(nn5)C6CCCCC6)O)O
CACTVS 3.385Cc1cc(cc(C)c1O)C(=O)NC[C@@H](O)[C@@H](O)[C@@H]2O[C@@](C[C@H](O)[C@H]2NC(=O)Cn3cc(nn3)C4CCCCC4)(OC[C@H]5O[C@@H](O[C@H]6[C@H](O)[C@@H](O)[C@H](OCCN)O[C@@H]6CO)[C@H](O)[C@@H](O)[C@H]5O)C(O)=O
FormulaC42 H64 N6 O20
Name2-aminoethyl 5-{[(4-cyclohexyl-1H-1,2,3-triazol-1-yl)acetyl]amino}-3,5,9-trideoxy-9-[(4-hydroxy-3,5-dimethylbenzene-1-carbonyl)amino]-D-glycero-alpha-D-galacto-non-2-ulopyranonosyl-(2->6)-beta-D-galactopyranosyl-(1->4)-beta-D-glucopyranoside
ChEMBL
DrugBank
ZINC
PDB chain6d4a Chain A Residue 203 [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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PDB6d4a Small Molecule Binding to Alzheimer Risk Factor CD33 Promotes A beta Phagocytosis.
Resolution1.751 Å
Binding residue
(original residue number in PDB)
F21 F117 R119 K126 Y127 S128 K130
Binding residue
(residue number reindexed from 1)
F2 F98 R100 K107 Y108 S109 K111
Annotation score1
Binding affinityMOAD: Kd=118uM
PDBbind-CN: -logKd/Ki=3.93,Kd=118uM
Enzymatic activity
Enzyme Commision number ?
External links
PDB RCSB:6d4a, PDBe:6d4a, PDBj:6d4a
PDBsum6d4a
PubMed31369984
UniProtP20138|CD33_HUMAN Myeloid cell surface antigen CD33 (Gene Name=CD33)

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