Structure of PDB 4cd4 Chain A Binding Site BS02

Receptor Information

>4cd4 Chain A (length=367) Species: 498211 (Cellvibrio japonicus Ueda107)

LPALIDTQATAETRALYRNLAKLRYKHLLFGHEDSLAYGVHWEGDMDRSD
VRDVTGANPAVYGWELGGLELGHTANLDAVNFEKMQHWIKAGYSRGGVIT
ISWHVFNPVSGGNSWDKTPAVHELIPGGARHATLKAYLDTFVAFNEGLAD
VDAQGNKHYPPIIFRPWHEHNGDWFWWGKGHASEQDYIALWRFTVHYLRD
EKKLRNLIYAYSPDRSRIDMANFEAGYLYGYPGDAYVDIIGLDNYWDVGH
EANTASADEQKAALTASLKQLVQIARSKGKIAALTETGNNRLTIDNFWTE
RLLGPISADADASEIAYVMVWRNANLAREKSEQFFAPFPGQATADDFKRF
YQSEVVLFEDELPPLYR

Ligand information

• Ligand ID: IFM
• InChI: InChI=1S/C6H13NO3/c8-3-4-1-7-2-5(9)6(4)10/h4-10H,1-3H2/t4-,5-,6-/m1/s1
• InChIKey: QPYJXFZUIJOGNX-HSUXUTPPSA-N
• SMILES:
  CACTVS 3.341: OC[CH]1CNC[CH](O)[CH]1O
  OpenEye OEToolkits 1.5.0: C1[C@@H]([C@H]([C@@H](CN1)O)O)CO
  ACDLabs 10.04: OC1C(CO)CNCC1O
  CACTVS 3.341: OC[C@H]1CNC[C@@H](O)[C@@H]1O
  OpenEye OEToolkits 1.5.0: C1C(C(C(CN1)O)O)CO
• Formula: C6 H13 N O3
• Name: 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE;
  Afegostat;
  isofagomine;
  (3R,4R,5R)-5-(HYDROXYMETHYL)PIPERIDINE-3,4-DIOL
• ChEMBL: CHEMBL206468
• DrugBank: DB04545
• ZINC: ZINC000003813668
• PDB chain: 4cd4 Chain A Residue 1423

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4cd4 Combined Inhibitor Free-Energy Landscape and Structural Analysis Reports on the Mannosidase Conformational Coordinate.
• Resolution: 1.2 Å
• Binding residue (original residue number in PDB): H156 E221 Y297 E338 W373
• Binding residue (residue number reindexed from 1): H104 E169 Y245 E286 W321
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=6.58,Ki=263nM

Enzymatic activity

• Enzyme Commision number: 3.2.1.78: mannan endo-1,4-beta-mannosidase.

Gene Ontology

Molecular Function

• GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
• GO:0016985 mannan endo-1,4-beta-mannosidase activity

Biological Process

• GO:0006080 substituted mannan metabolic process

External links

• PDB: RCSB:4cd4, PDBe:4cd4, PDBj:4cd4
• PDBsum: 4cd4
• PubMed: 24339341
• UniProt: B3PGI1