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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:

3px2

1.650 Å

X-ray

2010-12-09

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase
ID:TYLM1_STRFR
AC:P95748
Organism:Streptomyces fradiae
Reign:Bacteria
TaxID:1906
EC Number:2.1.1.235


Chains:

Chain Name:Percentage of Residues
within binding site
D100 %


Ligand binding site composition:

B-Factor:8.883
Number of residues:37
Including
Standard Amino Acids: 34
Non Standard Amino Acids: 1
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.9571069.875

% Hydrophobic% Polar
47.0053.00
According to VolSite

Ligand :
3px2_2 Structure
HET Code: T3Q
Formula: C16H26N3O14P2
Molecular weight: 546.337 g/mol
DrugBank ID: -
Buried Surface Area:67.44 %
Polar Surface area: 283.77 Å2
Number of
H-Bond Acceptors: 14
H-Bond Donors: 5
Rings: 3
Aromatic rings: 0
Anionic atoms: 2
Cationic atoms: 1
Rule of Five Violation: 2
Rotatable Bonds: 8

Mass center Coordinates

XYZ
-1.150092.119717.78049


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
O4QOHTYR- 142.65172.93H-Bond
(Ligand Donor)
C4QCZTYR- 144.480Hydrophobic
O1ANZLYS- 292.97151.98H-Bond
(Protein Donor)
O1ANZLYS- 292.970Ionic
(Protein Cationic)
O2BNZLYS- 292.870Ionic
(Protein Cationic)
N3QOPHE- 1183.17152.43H-Bond
(Ligand Donor)
C2QCZPHE- 1184.30Hydrophobic
C1'CH2TRP- 1524.350Hydrophobic
C4'CH2TRP- 1523.790Hydrophobic
C2QCZ3TRP- 1523.960Hydrophobic
C5MCZ2TRP- 1534.320Hydrophobic
C1'CE2TRP- 1533.850Hydrophobic
O4'NE1TRP- 1533142.2H-Bond
(Protein Donor)
C1'CD1PHE- 1584.410Hydrophobic
C2'CE1PHE- 1584.140Hydrophobic
O2NTHR- 1593.02168.99H-Bond
(Protein Donor)
C5MCZTYR- 1623.920Hydrophobic
C5'CE1TYR- 1624.030Hydrophobic
C2'CD1TYR- 1623.580Hydrophobic
O2ANH2ARG- 1772.9144.22H-Bond
(Protein Donor)
O2ANH1ARG- 1772.83148H-Bond
(Protein Donor)
O2ACZARG- 1773.310Ionic
(Protein Cationic)
O3'OGSER- 1812.7156.44H-Bond
(Ligand Donor)
C3'CBSER- 1814.090Hydrophobic
C6QCG2ILE- 1904.080Hydrophobic
C3'CD1ILE- 1904.060Hydrophobic
C6QCG2VAL- 1924.370Hydrophobic
C4QCD1ILE- 2124.450Hydrophobic
C2QCD1ILE- 2124.460Hydrophobic
O1BCZARG- 2413.870Ionic
(Protein Cationic)
O1BNH2ARG- 2412.7139H-Bond
(Protein Donor)
O2QNH1ARG- 2412.76171.19H-Bond
(Protein Donor)