Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

3anp

1.950 Å

X-ray

2010-09-06

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Transcriptional repressor, TetR family
ID:Q5SM42_THET8
AC:Q5SM42
Organism:Thermus thermophilus
Reign:Bacteria
TaxID:300852
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A23 %
B77 %


Ligand binding site composition:

B-Factor:21.274
Number of residues:48
Including
Standard Amino Acids: 48
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.164560.250

% Hydrophobic% Polar
69.2830.72
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median3anpHydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy80255075Highcharts.com
Ligand :
3anp_1 Structure
HET Code: DCC
Formula: C33H54N7O17P3S
Molecular weight: 945.805 g/mol
DrugBank ID: DB03264
Buried Surface Area:45.27 %
Polar Surface area: 429.68 Å2
Number of
H-Bond Acceptors: 22
H-Bond Donors: 5
Rings: 3
Aromatic rings: 2
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 30

Mass center Coordinates

XYZ
38.697338.769717.5604
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median3anpRingsAromatic RingsHBond AcceptorHBond DonorRotatable BondsPositive IonizableNegativeIonizableRO5 Violation802040Highcharts.com


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
C12CBLEU- 644.220Hydrophobic
C10CD2LEU- 934.230Hydrophobic
C12CD2LEU- 933.930Hydrophobic
C11CD2LEU- 1044.20Hydrophobic
C11CEMET- 1074.220Hydrophobic
CA9CEMET- 1073.910Hydrophobic
CA9CE1PHE- 1084.270Hydrophobic
CA2CD1LEU- 1114.440Hydrophobic
CA5CD1LEU- 1113.560Hydrophobic
SCD2LEU- 1124.320Hydrophobic
OP2NEARG- 1203.3135.11H-Bond
(Protein Donor)
CP7CD2PHE- 1233.820Hydrophobic
CP9CE1PHE- 1233.730Hydrophobic
CA3CE1PHE- 1233.520Hydrophobic
CA7CBLEU- 1264.080Hydrophobic
CA6CBLEU- 1284.230Hydrophobic
CA8CBLEU- 1284.050Hydrophobic
O32OGSER- 1502.85150.27H-Bond
(Protein Donor)
O33NEARG- 1533.17164.41H-Bond
(Protein Donor)
CA9CE2TYR- 1623.90Hydrophobic
CA8CE2TYR- 1623.680Hydrophobic
SCE2PHE- 1633.760Hydrophobic
CA2CGPHE- 1633.560Hydrophobic
CA5CBPHE- 1634.030Hydrophobic
SCD2LEU- 1643.970Hydrophobic
CP8CDARG- 1684.410Hydrophobic
CP9CDARG- 1683.870Hydrophobic
CP4CGARG- 1684.50Hydrophobic
CP1CBARG- 1684.480Hydrophobic
OA1NH2ARG- 1682.76145.88H-Bond
(Protein Donor)
CP4CGTYR- 1723.440Hydrophobic
CP8CG2THR- 1733.70Hydrophobic
O22NH1ARG- 1762.97138.64H-Bond
(Protein Donor)
O22NH2ARG- 1762.82146.04H-Bond
(Protein Donor)
O22CZARG- 1763.310Ionic
(Protein Cationic)
DuArCZARG- 1763.31176.37Pi/Cation