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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:

2g0b

3.000 Å

X-ray

2006-02-11

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Long-chain N-acyl amino acid synthase
ID:Q8KNZ7_9BACT
AC:Q8KNZ7
Organism:uncultured bacterium CSLC2
Reign:Bacteria
TaxID:1091571
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
E97 %
F3 %


Ligand binding site composition:

B-Factor:40.370
Number of residues:39
Including
Standard Amino Acids: 39
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.575651.375

% Hydrophobic% Polar
66.8433.16
According to VolSite

Ligand :
2g0b_5 Structure
HET Code: NLT
Formula: C21H32NO4
Molecular weight: 362.483 g/mol
DrugBank ID: DB08275
Buried Surface Area:72.52 %
Polar Surface area: 89.46 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 2
Rings: 1
Aromatic rings: 1
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 14

Mass center Coordinates

XYZ
41.676597.05429.8917


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
O2OHTYR- 272.83164.73H-Bond
(Protein Donor)
C5CD1ILE- 623.850Hydrophobic
C7CG1VAL- 953.690Hydrophobic
ONGLN- 973.31156.71H-Bond
(Protein Donor)
OLNPHE- 983.25141.71H-Bond
(Protein Donor)
C4CBPHE- 983.780Hydrophobic
C11CE2PHE- 1163.930Hydrophobic
C6CE2PHE- 1223.850Hydrophobic
C11CBPHE- 1224.330Hydrophobic
C8CD2PHE- 1223.690Hydrophobic
C9CG1VAL- 1254.160Hydrophobic
C11CBLEU- 1264.410Hydrophobic
C10CD2LEU- 1374.210Hydrophobic
C6CD1ILE- 1393.710Hydrophobic
C7CD1ILE- 1393.70Hydrophobic
NOSER- 1403.07144.78H-Bond
(Ligand Donor)
C2CG2ILE- 1413.690Hydrophobic
OHND2ASN- 1422.78128.38H-Bond
(Protein Donor)
CZCBASN- 1423.90Hydrophobic
C4CZTYR- 1493.970Hydrophobic
C6CE2TYR- 1493.680Hydrophobic
C8CZPHE- 1544.120Hydrophobic
C10CZPHE- 1543.760Hydrophobic
C12CE1PHE- 1544.160Hydrophobic
CBCE2TYR- 1634.120Hydrophobic
CGCG2VAL- 1664.20Hydrophobic
CE2CG1VAL- 1663.70Hydrophobic
CZCBALA- 1684.060Hydrophobic
OHOPRO- 1692.96152.69H-Bond
(Ligand Donor)
CE1CBALA- 1704.070Hydrophobic
C12CD2LEU- 1753.850Hydrophobic