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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Protein Data Bank Entry:

2std

2.100 Å

X-ray

1997-12-21

Activity from ChEMBL: What is pChEMBL ?
MinMeanMedianStandard DeviationMaxCount
pChEMBL:10.52010.52010.5200.00010.5201

List of CHEMBLId :

CHEMBL147792


Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Scytalone dehydratase
ID:SCYD_MAGO7
AC:P56221
Organism:Magnaporthe oryzae
Reign:Eukaryota
TaxID:242507
EC Number:4.2.1.94


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:33.160
Number of residues:33
Including
Standard Amino Acids: 32
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.721303.750

% Hydrophobic% Polar
73.3326.67
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median2stdHydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy80204060Highcharts.com
Ligand :
2std_1 Structure
HET Code: CRP
Formula: C15H18Cl3NO
Molecular weight: 334.669 g/mol
DrugBank ID: DB02946
Buried Surface Area:79.7 %
Polar Surface area: 29.1 Å2
Number of
H-Bond Acceptors: 1
H-Bond Donors: 1
Rings: 2
Aromatic rings: 1
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 4

Mass center Coordinates

XYZ
29.592437.312622.4937
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median2stdRingsAromatic RingsHBond AcceptorHBond DonorRotatable BondsPositive IonizableNegativeIonizableRO5 Violation80510Highcharts.com


Binding mode :
What is Poseview ?
  • 2D View
  • 3D View
Binding mode
BioSolveIT Image generated by PoseView
Protein
Binding Site
Ligand
Interaction pattern
hydrophobic (CA)
aromatic (CZ)
hydrogen bond acceptor (O)
hydrogen bond acceptor/donor (OG)
hydrogen bond donor (N)
positively ionized (NZ)
negatively ionized (OD1)
metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT
BioSolveIT


LigandProteinInteraction
AtomAtomResidueDistance
(Å)
Angle (°)Type
CL1CH2TRP- 263.540Hydrophobic
C8'CE2TYR- 303.860Hydrophobic
CL1CE2TYR- 304.430Hydrophobic
C5CZPHE- 534.350Hydrophobic
C6CE2PHE- 534.030Hydrophobic
CL0CD1LEU- 544.110Hydrophobic
C3'CGMET- 694.150Hydrophobic
C8'CG1VAL- 704.390Hydrophobic
C8'CG1VAL- 753.480Hydrophobic
C4'CG2VAL- 753.860Hydrophobic
C6'CG1VAL- 753.430Hydrophobic
C8'CD1LEU- 763.680Hydrophobic
CL1CD1LEU- 10640Hydrophobic
C4CG1VAL- 1083.40Hydrophobic
C4CBALA- 1273.770Hydrophobic
CL2CBSER- 1294.230Hydrophobic
CL1CD2LEU- 1473.930Hydrophobic
CL2CBPRO- 1493.850Hydrophobic
CL2CD1ILE- 1514.250Hydrophobic
C5CD1ILE- 1513.740Hydrophobic
C4CH2TRP- 1534.490Hydrophobic
C6CH2TRP- 1533.90Hydrophobic
CL0CZPHE- 1583.610Hydrophobic
C6CD1PHE- 1584.160Hydrophobic
CL0CD2PHE- 1693.880Hydrophobic
NOHOH- 2762.98164.86H-Bond
(Ligand Donor)