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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:

4mv8

2.060 Å

X-ray

2013-09-23

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Biotin carboxylase
ID:ACCC_HAEIN
AC:P43873
Organism:Haemophilus influenzae
Reign:Bacteria
TaxID:71421
EC Number:6.3.4.14


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:69.071
Number of residues:30
Including
Standard Amino Acids: 30
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.414681.750

% Hydrophobic% Polar
40.5959.41
According to VolSite

Ligand :
4mv8_1 Structure
HET Code: ACP
Formula: C11H14N5O12P3
Molecular weight: 501.176 g/mol
DrugBank ID: DB03909
Buried Surface Area:49.31 %
Polar Surface area: 310.64 Å2
Number of
H-Bond Acceptors: 16
H-Bond Donors: 3
Rings: 3
Aromatic rings: 2
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 8

Mass center Coordinates

XYZ
-78.121927.3686-9.78068


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
O1ANZLYS- 1162.98149.13H-Bond
(Protein Donor)
O1ANZLYS- 1162.980Ionic
(Protein Cationic)
N7NZLYS- 1592.96154.87H-Bond
(Protein Donor)
C4'SDMET- 1694.450Hydrophobic
C1'CEMET- 16940Hydrophobic
N6OE2GLU- 2013.07156.97H-Bond
(Ligand Donor)
N6OLYS- 2022.81148.26H-Bond
(Ligand Donor)
N1NLEU- 2043.14168.19H-Bond
(Protein Donor)
C2'CD2LEU- 2784.420Hydrophobic
C3'CD1ILE- 2874.490Hydrophobic
C2'CD1ILE- 4374.010Hydrophobic