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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:

2imk

1.900 Å

X-ray

2006-10-02

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:AGAP009194-PA
ID:Q7PVS6_ANOGA
AC:Q7PVS6
Organism:Anopheles gambiae
Reign:Eukaryota
TaxID:7165
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A18 %
B82 %


Ligand binding site composition:

B-Factor:21.205
Number of residues:39
Including
Standard Amino Acids: 39
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.032843.750

% Hydrophobic% Polar
65.6034.40
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median2imkHydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy80204060Highcharts.com
Ligand :
2imk_2 Structure
HET Code: GTX
Formula: C16H28N3O6S
Molecular weight: 390.475 g/mol
DrugBank ID: -
Buried Surface Area:59.25 %
Polar Surface area: 191.4 Å2
Number of
H-Bond Acceptors: 7
H-Bond Donors: 3
Rings: 0
Aromatic rings: 0
Anionic atoms: 2
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 15

Mass center Coordinates

XYZ
4.0843513.03130.0052
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median2imkRingsAromatic RingsHBond AcceptorHBond DonorRotatable BondsPositive IonizableNegativeIonizableRO5 Violation801020Highcharts.com


Binding mode :
What is Poseview ?
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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
C6SCD2LEU- 94.050Hydrophobic
C6SCD2LEU- 113.570Hydrophobic
SG2CBSER- 124.270Hydrophobic
C4SCBSER- 124.140Hydrophobic
CG1CGPRO- 143.920Hydrophobic
SG2CGPRO- 143.830Hydrophobic
CB2CD1LEU- 363.680Hydrophobic
C3SCD1LEU- 363.850Hydrophobic
O31ND1HIS- 533.09137.5H-Bond
(Protein Donor)
CG1CBTHR- 543.820Hydrophobic
N2OILE- 553.16147.29H-Bond
(Ligand Donor)
O2NILE- 552.96161.07H-Bond
(Protein Donor)
CB2CG1ILE- 554.180Hydrophobic
N1OE1GLU- 672.79156.87H-Bond
(Ligand Donor)
N1OE1GLU- 672.790Ionic
(Ligand Cationic)
O11NSER- 682.94167.47H-Bond
(Protein Donor)
O12OGSER- 682.75172.08H-Bond
(Protein Donor)
CB1CE1PHE- 1083.740Hydrophobic
CG1CZPHE- 1084.290Hydrophobic
SG2CZPHE- 1083.740Hydrophobic
OE1NH2ARG- 1122.89120.31H-Bond
(Protein Donor)
O32NH1ARG- 1123.38147.1H-Bond
(Protein Donor)
O32NH2ARG- 1123.26154.43H-Bond
(Protein Donor)
O32CZARG- 1123.780Ionic
(Protein Cationic)
C5SCD1LEU- 1193.910Hydrophobic
C5SCD1LEU- 2073.570Hydrophobic