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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:

2z3u

2.400 Å

X-ray

2007-06-06

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Cytochrome P450
ID:Q83WG3_9ACTN
AC:Q83WG3
Organism:Streptomyces sp. TP-A0274
Reign:Bacteria
TaxID:171258
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:17.795
Number of residues:37
Including
Standard Amino Acids: 29
Non Standard Amino Acids: 2
Water Molecules: 6
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.792891.000

% Hydrophobic% Polar
64.3935.61
According to VolSite

Ligand :
2z3u_1 Structure
HET Code: CRR
Formula: C22H13N3O4
Molecular weight: 383.356 g/mol
DrugBank ID: DB07588
Buried Surface Area:78.14 %
Polar Surface area: 127.63 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 3
Rings: 5
Aromatic rings: 5
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 4

Mass center Coordinates

XYZ
-9.29362-1.69483-25.0003


Binding mode :
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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
O37NH2ARG- 672.96134.34H-Bond
(Protein Donor)
C3CG1VAL- 944.130Hydrophobic
C2CG2VAL- 944.310Hydrophobic
C17CG1VAL- 994.410Hydrophobic
C1CD1LEU- 1824.420Hydrophobic
N3OE1GLN- 1833.01150.09H-Bond
(Ligand Donor)
C2CBALA- 1854.120Hydrophobic
O39OGSER- 1862.69162.53H-Bond
(Protein Donor)
C20CBSER- 1863.950Hydrophobic
O39NTHR- 1872.91161.88H-Bond
(Protein Donor)
C16CBALA- 2543.950Hydrophobic
C15CG2THR- 2584.390Hydrophobic
C13CG1VAL- 3014.150Hydrophobic
C14CG2VAL- 3013.790Hydrophobic
O37NTHR- 3053.22149.54H-Bond
(Protein Donor)
C13CG1VAL- 4024.360Hydrophobic
N2OHOH- 6443.2145.79H-Bond
(Ligand Donor)