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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:

4amb

2.620 Å

X-ray

2012-03-08

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Putative glycosyl transferase
ID:Q9RN61_STRNO
AC:Q9RN61
Organism:Streptomyces nogalater
Reign:Bacteria
TaxID:38314
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:31.781
Number of residues:34
Including
Standard Amino Acids: 34
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.5831856.250

% Hydrophobic% Polar
45.6454.36
According to VolSite

Ligand :
4amb_1 Structure
HET Code: DUD
Formula: C9H11N2O11P2
Molecular weight: 385.138 g/mol
DrugBank ID: DB03413
Buried Surface Area:62.87 %
Polar Surface area: 220.27 Å2
Number of
H-Bond Acceptors: 11
H-Bond Donors: 2
Rings: 2
Aromatic rings: 0
Anionic atoms: 3
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 6

Mass center Coordinates

XYZ
-40.196825.3375-21.1861


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
C4'CD1LEU- 274.380Hydrophobic
O3'ND2ASN- 2123.23136.11H-Bond
(Protein Donor)
C1'CBASN- 2124.250Hydrophobic
O1BOGSER- 2363.44161.87H-Bond
(Protein Donor)
N3OILE- 2862.53168.33H-Bond
(Ligand Donor)
O4NILE- 2863.47159.75H-Bond
(Protein Donor)
O2NLEU- 2882.79132.04H-Bond
(Protein Donor)
C2'CBLEU- 2883.810Hydrophobic
O1ANE2HIS- 3013.08125.46H-Bond
(Protein Donor)
O2BNE2HIS- 3013.16158.57H-Bond
(Protein Donor)
O2ANGLY- 3052.65141.43H-Bond
(Protein Donor)
O5'OG1THR- 3063.35126.45H-Bond
(Protein Donor)
O1AOG1THR- 3063.4174.82H-Bond
(Protein Donor)