Home Research COVID-19 Services Publications People Teaching Job Opening News Forum Lab Only
Online Services

●I-TASSER ●I-TASSER-MTD ●C-I-TASSER ●CR-I-TASSER ●QUARK ●C-QUARK ●LOMETS ●MUSTER ●CEthreader ●SEGMER ●DeepFold ●DeepFoldRNA ●FoldDesign ●COFACTOR ●COACH ●MetaGO ●TripletGO ●IonCom ●FG-MD ●ModRefiner ●REMO ●DEMO ●DEMO-EM ●SPRING ●COTH ●Threpp ●PEPPI ●BSpred ●ANGLOR ●EDock ●BSP-SLIM ●SAXSTER ●FUpred ●ThreaDom ●ThreaDomEx ●EvoDesign ●BindProf ●BindProfX ●SSIPe ●GPCR-I-TASSER ●MAGELLAN ●ResQ ●STRUM ●DAMpred

●TM-score ●TM-align ●US-align ●MM-align ●RNA-align ●NW-align ●LS-align ●EDTSurf ●MVP ●MVP-Fit ●SPICKER ●HAAD ●PSSpred ●3DRobot ●MR-REX ●I-TASSER-MR ●SVMSEQ ●NeBcon ●ResPRE ●TripletRes ●DeepPotential ●WDL-RF ●ATPbind ●DockRMSD ●DeepMSA ●FASPR ●EM-Refiner ●GPU-I-TASSER

●BioLiP ●E. coli ●GLASS ●GPCR-HGmod ●GPCR-RD ●GPCR-EXP ●Tara-3D ●TM-fold ●DECOYS ●POTENTIAL ●RW/RWplus ●EvoEF ●HPSF ●THE-DB ●ADDRESS ●Alpaca-Antibody ●CASP7 ●CASP8 ●CASP9 ●CASP10 ●CASP11 ●CASP12 ●CASP13 ●CASP14

BioLiP

Structure of PDB 2oym Chain B Binding Site BS01

Receptor Information
>2oym Chain B (length=434) Species: 1831 (Rhodococcus sp. (in: high G+C Gram-positive bacteria)) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PSYLKDDDGRSLILRGFNTASSAKSAPDGMPQFTEADLAREYADMGTNFV
RFLISWRSVEPAPGVYDQQYLDRVEDRVGWYAERGYKVMLDMHQDVYSGA
ITPIGNGAPAWATYMDGLPVEPQPRWELYYIQPGVMRAFDNFWNTTGKHP
ELVEHYAKAWRAVADRFADNDAVVAYDLMNEPFGGSLQGPAFEAGPLAAM
YQRTTDAIRQVDQDTWVCVAPQAIGVNQGLPSGLTKIDDPRAGQQRIAYC
PHLYPLPLDHEGLARTLTDVTIDAWRANTAHTARVLGDVPIILGEFGLDT
TLPGARDYIERVYGTAREMGAGVSYWSSDPGPWGPYLPDGTQTLLVDTLN
KPYPRAVAGTPTEWSSTSDRLQLTIEPDAAITAPTEIYLPEAGFPGDVHV
EGADVVGWDRQSRLLTVRTPADSGNVTVTVTPAA
Ligand information
Ligand IDMNI
InChIInChI=1S/C15H23N3O4/c1-18(2)10-5-3-9(4-6-10)15(22)16-7-11-13(20)14(21)12(8-19)17-11/h3-6,11-14,17,19-21H,7-8H2,1-2H3,(H,16,22)/t11-,12-,13-,14-/m1/s1
InChIKeyOULLPOCYJLHTGG-AAVRWANBSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(c1ccc(N(C)C)cc1)NCC2NC(CO)C(O)C2O
OpenEye OEToolkits 1.5.0CN(C)c1ccc(cc1)C(=O)NC[C@@H]2[C@H]([C@@H]([C@H](N2)CO)O)O
CACTVS 3.341CN(C)c1ccc(cc1)C(=O)NC[CH]2N[CH](CO)[CH](O)[CH]2O
CACTVS 3.341CN(C)c1ccc(cc1)C(=O)NC[C@H]2N[C@H](CO)[C@@H](O)[C@@H]2O
OpenEye OEToolkits 1.5.0CN(C)c1ccc(cc1)C(=O)NCC2C(C(C(N2)CO)O)O
FormulaC15 H23 N3 O4
NameN-{[(2R,3R,4R,5R)-3,4-DIHYDROXY-5-(HYDROXYMETHYL)PYRROLIDIN-2-YL]METHYL}-4-(DIMETHYLAMINO)BENZAMIDE;
1-(4-DIMETHYLAMINO)BENZOYLAMINO-1,2,5-TRIDEOXY-2,5-IMINO-D-MANNITOL
ChEMBL
DrugBank
ZINCZINC000016052336
PDB chain2oym Chain B Residue 600 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB2oym The structural basis of glycosidase inhibition by five-membered iminocyclitols: the clan a glycoside hydrolase endoglycoceramidase as a model system.
Resolution1.86 Å
Binding residue
(original residue number in PDB)		H135 D137 W178 E179 Y182 N232 E233 F235 Y306 E351 W382
Binding residue
(residue number reindexed from 1)		H93 D95 W126 E127 Y130 N180 E181 F183 Y254 E295 W326
Annotation score1
Binding affinityMOAD: Ki=10uM
Enzymatic activity
Enzyme Commision number 3.2.1.123: endoglycosylceramidase.
Gene Ontology
Molecular Function
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0047876 endoglycosylceramidase activity
Biological Process
GO:0000272 polysaccharide catabolic process
GO:0005975 carbohydrate metabolic process
GO:0016042 lipid catabolic process
GO:1901136 carbohydrate derivative catabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links

zhanglabzhanggroup.org | +65-6601-1241 | Computing 1, 13 Computing Drive, Singapore 117417