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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:

2bd0

1.700 Å

X-ray

2005-10-19

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Sepiapterin reductase
ID:SPRE_CHLTE
AC:Q8KES3
Organism:Chlorobium tepidum
Reign:Bacteria
TaxID:194439
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
D100 %


Ligand binding site composition:

B-Factor:21.170
Number of residues:24
Including
Standard Amino Acids: 23
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors: NAP
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.893337.500

% Hydrophobic% Polar
65.0035.00
According to VolSite

Ligand :
2bd0_1 Structure
HET Code: BIO
Formula: C9H11N5O3
Molecular weight: 237.215 g/mol
DrugBank ID: DB03886
Buried Surface Area:63.77 %
Polar Surface area: 133.72 Å2
Number of
H-Bond Acceptors: 7
H-Bond Donors: 4
Rings: 2
Aromatic rings: 1
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
35.719736.054115.8405


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
O9OGSER- 1452.93163.06H-Bond
(Protein Donor)
C11CG2VAL- 1463.330Hydrophobic
C11CBALA- 1473.730Hydrophobic
C11CE1PHE- 1523.80Hydrophobic
O9OHTYR- 1582.82121.33H-Bond
(Ligand Donor)
C9CE2TYR- 15840Hydrophobic
N2OMET- 1953.41157.76H-Bond
(Ligand Donor)
C9C4NNAP- 38003.570Hydrophobic