Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

3d2p

2.560 Å

X-ray

2008-05-08

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Amino-acid acetyltransferase
ID:Q5FAK7_NEIG1
AC:Q5FAK7
Organism:Neisseria gonorrhoeae
Reign:Bacteria
TaxID:242231
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:28.930
Number of residues:30
Including
Standard Amino Acids: 30
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.1861127.250

% Hydrophobic% Polar
41.0258.98
According to VolSite

Ligand :
3d2p_1 Structure
HET Code: COA
Formula: C21H32N7O16P3S
Molecular weight: 763.502 g/mol
DrugBank ID: DB01992
Buried Surface Area:44.21 %
Polar Surface area: 426.11 Å2
Number of
H-Bond Acceptors: 21
H-Bond Donors: 6
Rings: 3
Aromatic rings: 2
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 3
Rotatable Bonds: 18

Mass center Coordinates

XYZ
-12.273959.987421.6623


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
C6PCD1LEU- 3073.330Hydrophobic
CDPCGLEU- 3574.190Hydrophobic
S1PCBLEU- 3573.950Hydrophobic
CDPCG2VAL- 3593.880Hydrophobic
CAPCGGLN- 3644.420Hydrophobic
O4ANASP- 3652.79154.95H-Bond
(Protein Donor)
O2ANGLY- 3673.04158.29H-Bond
(Protein Donor)
O5ANGLY- 3692.86143.47H-Bond
(Protein Donor)
O1ANGLU- 3703.05154.14H-Bond
(Protein Donor)
N6AOASN- 3943.13163.85H-Bond
(Ligand Donor)
CEPCG2THR- 3953.580Hydrophobic
O5BNE1TRP- 3983.11165.99H-Bond
(Protein Donor)
CCPCZ2TRP- 3983.80Hydrophobic
CEPCD2TRP- 3984.290Hydrophobic