Structure of PDB 6ghv Chain F Binding Site BS02

Receptor Information
>6ghv Chain F (length=132) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
CHPCPWEWTFFQGNCYFMSNSQRNWHDSITACKEVGAQLVVIKSAEEQNF
LQLQSSRSNRFTWMGLSDLNQEGTWQWVDGSPLLPSFKQYWNRGEPNNVG
EEDCAEFSGNGWNDDKCNLAKFWICKKSAASC
Ligand information
Ligand IDEZ8
InChIInChI=1S/C35H47ClN6O10/c36-9-10-50-27-11-25(33(48)38-14-20-1-5-22(17-43)6-2-20)26(34(49)39-15-21-3-7-23(18-44)8-4-21)12-28(27)51-35-30(42-16-24(13-37)40-41-42)32(47)31(46)29(19-45)52-35/h1-8,16,25-32,35,43-47H,9-15,17-19,37H2,(H,38,48)(H,39,49)/p+1/t25-,26-,27-,28-,29+,30-,31+,32+,35-/m0/s1
InChIKeyBYGZQFCUFRSCML-RWSQSUCKSA-O
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1cc(ccc1CNC(=O)C2CC(C(CC2C(=O)NCc3ccc(cc3)CO)OC4C(C(C(C(O4)CO)O)O)n5cc(nn5)C[NH3+])OCCCl)CO
CACTVS 3.385[NH3+]Cc1cn(nn1)[CH]2[CH](O)[CH](O)[CH](CO)O[CH]2O[CH]3C[CH]([CH](C[CH]3OCCCl)C(=O)NCc4ccc(CO)cc4)C(=O)NCc5ccc(CO)cc5
OpenEye OEToolkits 2.0.6c1cc(ccc1CNC(=O)[C@H]2C[C@@H]([C@H](C[C@@H]2C(=O)NCc3ccc(cc3)CO)O[C@@H]4[C@H]([C@H]([C@@H]([C@H](O4)CO)O)O)n5cc(nn5)C[NH3+])OCCCl)CO
CACTVS 3.385[NH3+]Cc1cn(nn1)[C@H]2[C@@H](O)[C@H](O)[C@@H](CO)O[C@@H]2O[C@H]3C[C@@H]([C@H](C[C@@H]3OCCCl)C(=O)NCc4ccc(CO)cc4)C(=O)NCc5ccc(CO)cc5
FormulaC35 H48 Cl N6 O10
Name[1-[(2~{S},3~{S},4~{R},5~{S},6~{R})-2-[(1~{S},2~{S},4~{S},5~{S})-2-(2-chloroethyloxy)-4,5-bis[[4-(hydroxymethyl)phenyl]methylcarbamoyl]cyclohexyl]oxy-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-3-yl]-1,2,3-triazol-4-yl]methylazanium
ChEMBL
DrugBank
ZINC
PDB chain6ghv Chain F Residue 502 [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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PDB6ghv Enhancing Potency and Selectivity of a DC-SIGN Glycomimetic Ligand by Fragment-Based Design: Structural Basis.
Resolution2.1 Å
Binding residue
(original residue number in PDB)
F313 E347 N349 V351 G352 E354 E358 N365 D367 K368
Binding residue
(residue number reindexed from 1)
F61 E95 N97 V99 G100 E102 E106 N113 D115 K116
Annotation score1
Binding affinityMOAD: Kd=52uM
Enzymatic activity
Enzyme Commision number ?
External links
PDB RCSB:6ghv, PDBe:6ghv, PDBj:6ghv
PDBsum6ghv
PubMed31469191
UniProtQ9NNX6|CD209_HUMAN CD209 antigen (Gene Name=CD209)

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