PDB Entry (3gdn)

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Visualizer: MichelaNGLo

PDB ID: 3gdn Resolution: 1.67 Å Exp. Method: X-RAY DIFFRACTION
PMID: 19256550 DOI: 10.1021/bi802162s
Protein
Protein Name: (R)-mandelonitrile lyase 2
Protein Class: LIGASE
Uniprot ID/ACC: Q945K2 (MDL2_PRUDU) Organism: Prunus dulcis
Gene Symbol: - Gene ID: -
Pocket Descriptors
Volume: 188.416 Depth: 21.5095
Hydrophobicity: 0.712 Drug Score: 0.0470923
Pocket Similarity: Calculate
Ligand
Ligand Name:   (2R)-hydroxy(phenyl)ethanenitrile
HET ID:   MXN PubChem:   9548674
DrugBank:   - ChEMBL:   CHEMBL1234541
Canonical SMILES:   O[C@H](c1ccccc1)C#N
Standard InChI:   InChI=1S/C8H7NO/c9-6-8(10)7-4-2-1-3-5-7/h1-5,8,10H/t8-/m0/s1
Molecular Formula:   C8H7NO Mol. Weight:   133.14728 Heavy Atoms:   10
Charge:   0 Is Chiral:   True logP:   1.24358
HBD:   1 HBA:   2 TPSA:   44.02
#Bonds:   11 #Rotatable Bonds:   1 Shape Complexity:   0.14285715
Stereocomplexity:   0.125 Ligand Type:   Small Molecule
Binding Affinity
-