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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:

3tso

1.800 Å

X-ray

2011-09-13

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Ras-related protein Rab-25
ID:RAB25_HUMAN
AC:P57735
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:22.627
Number of residues:39
Including
Standard Amino Acids: 35
Non Standard Amino Acids: 1
Water Molecules: 3
Cofactors:
Metals: MG

Cavity properties

LigandabilityVolume (Å3)
0.223614.250

% Hydrophobic% Polar
35.7164.29
According to VolSite

Ligand :
3tso_1 Structure
HET Code: GNP
Formula: C10H13N6O13P3
Molecular weight: 518.164 g/mol
DrugBank ID: DB02082
Buried Surface Area:77.28 %
Polar Surface area: 338.36 Å2
Number of
H-Bond Acceptors: 16
H-Bond Donors: 5
Rings: 3
Aromatic rings: 1
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 8

Mass center Coordinates

XYZ
-0.4972517.991714.9329


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
O1BNGLY- 243.06149.36H-Bond
(Protein Donor)
O3ANGLY- 243.19126.07H-Bond
(Protein Donor)
O3GNZLYS- 252.71145.4H-Bond
(Protein Donor)
O1BNLYS- 252.88158.66H-Bond
(Protein Donor)
O1BNZLYS- 252.94153.63H-Bond
(Protein Donor)
O3GNZLYS- 252.710Ionic
(Protein Cationic)
O1BNZLYS- 252.940Ionic
(Protein Cationic)
O2BNTHR- 263.04152.89H-Bond
(Protein Donor)
O1AND2ASN- 272.93123.84H-Bond
(Protein Donor)
O1ANASN- 273.09156.05H-Bond
(Protein Donor)
C2'CZPHE- 374.240Hydrophobic
O2'OSER- 382.62150.4H-Bond
(Ligand Donor)
O3'OHIS- 392.85149.55H-Bond
(Ligand Donor)
C3'CBSER- 414.370Hydrophobic
O1GOG1THR- 432.56175.06H-Bond
(Protein Donor)
O2GNTHR- 442.84162.02H-Bond
(Protein Donor)
O3GNGLY- 702.94157.31H-Bond
(Protein Donor)
N7ND2ASN- 1253.26137.89H-Bond
(Protein Donor)
O4'NZLYS- 1262.85129.73H-Bond
(Protein Donor)
N1OD2ASP- 1283.28128.22H-Bond
(Ligand Donor)
N1OD1ASP- 1282.72170.97H-Bond
(Ligand Donor)
N2OD2ASP- 1282.63167.14H-Bond
(Ligand Donor)
O6NLEU- 1573.35156.5H-Bond
(Protein Donor)
O2GMG MG- 2001.990Metal Acceptor
O2BMG MG- 2002.010Metal Acceptor