Structure of PDB 6hm1 Chain A Binding Site BS01

Receptor Information
>6hm1 Chain A (length=386) Species: 399741 (Serratia proteamaculans 568) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ASYLSVGYFNGGDINKLDVTQITHLNYSFGLIYNDEKQETNPALKDPSRL
HQIYLSPKVMADLQLLPVLRKQNPELKVLLSVGGWGARGFSGAAATAESR
AVFIRSVQQVIKQYHLDGIDLDWEYPVNGAWGLVESQPADRANFTLLLAE
LHKALDKGKLLTIAVGANVKSPQEWVDVKGIAPYLDYINLMTYDMAYGTQ
YFNSNLYDSKQWPTVAAADRYSANFVVDNYLAAGLKPAQLNLGIGFYGRV
PKRATEPGIDWDKADAAKNPVTQPYFTARETAVFKAMGLDLTKDSYFKYN
DIVSKLLNDPQRRFTAHWDSDAQVPYLTMKSAEGKPLFAISYENPRSVAL
KADYIKSKGLGGAMFWEYGADDNNRLAHQLAESLGI
Ligand information
Ligand IDAO3
InChIInChI=1S/C25H42N4O14/c1-8(33)26-14-17(36)16(35)11(6-31)39-23(14)42-22-12(7-32)40-24(15(19(22)38)27-9(2)34)41-21-10(5-30)20-13(18(21)37)28-25(43-20)29(3)4/h10-24,30-32,35-38H,5-7H2,1-4H3,(H,26,33)(H,27,34)/t10-,11+,12+,13+,14+,15+,16+,17-,18+,19-,20-,21+,22+,23-,24-/m0/s1
InChIKeyMDWNFWDBQGOKNZ-XYUDZHFQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(=O)N[C@@H]1[C@@H]([C@@H]([C@H](O[C@H]1O[C@@H]2[C@H](O[C@H]([C@@H]([C@@H]2O)NC(=O)C)O[C@@H]3[C@H]([C@H]4[C@@H]([C@H]3O)N=C(O4)N(C)C)CO)CO)CO)O)O
ACDLabs 10.04O=C(NC4C(O)C(O)C(OC4OC3C(OC(OC1C(O)C2N=C(OC2C1CO)N(C)C)C(NC(=O)C)C3O)CO)CO)C
OpenEye OEToolkits 1.5.0CC(=O)NC1C(C(C(OC1OC2C(OC(C(C2O)NC(=O)C)OC3C(C4C(C3O)N=C(O4)N(C)C)CO)CO)CO)O)O
CACTVS 3.341CN(C)C1=N[CH]2[CH](O)[CH](O[CH]3O[CH](CO)[CH](O[CH]4O[CH](CO)[CH](O)[CH](O)[CH]4NC(C)=O)[CH](O)[CH]3NC(C)=O)[CH](CO)[CH]2O1
CACTVS 3.341CN(C)C1=N[C@@H]2[C@@H](O)[C@H](O[C@@H]3O[C@H](CO)[C@@H](O[C@@H]4O[C@H](CO)[C@@H](O)[C@@H](O)[C@H]4NC(C)=O)[C@@H](O)[C@H]3NC(C)=O)[C@@H](CO)[C@@H]2O1
FormulaC25 H42 N4 O14
NameALLOSAMIDIN;
(3AR,4R,5R,6S,6AS)-2-(DIMETHYLAMINO)-3A,5,6,6A-TETRAHYDRO-4-HYDROXY-6-(HYDROXYMETHYL)-4H-CYCLOPENTOXAZOL-5-YL-2-(ACETYL AMINO)-4-O-[2-(ACETYLAMINO)-2-DEOXY-BETA-D-ALLOPYRANOSYL]-2-DEOXY-BETA-D-ALLOPYRANOSIDE
ChEMBLCHEMBL1230997
DrugBankDB04628
ZINCZINC000053683592
PDB chain6hm1 Chain A Residue 501 [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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PDB6hm1 Structural and Thermodynamic Signatures of Ligand Binding to the Enigmatic Chitinase D of Serratia proteamaculans.
Resolution1.54 Å
Binding residue
(original residue number in PDB)		Y28 F58 G113 W114 D151 E153 M220 Y222 D223 Y276 Y325 M393 W395
Binding residue
(residue number reindexed from 1)		Y8 F29 G84 W85 D122 E124 M191 Y193 D194 Y247 Y296 M364 W366
Annotation score1
Binding affinityMOAD: Kd=0.91uM
PDBbind-CN: -logKd/Ki=6.04,Kd=0.91uM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
GO:0008061 chitin binding
GO:0016798 hydrolase activity, acting on glycosyl bonds
Biological Process
GO:0005975 carbohydrate metabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6hm1, PDBe:6hm1, PDBj:6hm1
PDBsum6hm1
PubMed30789732
UniProtA8GFD6

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