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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:

3n10

1.600 Å

X-ray

2010-05-14

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Adenylate cyclase 2
ID:Q7CH76_YERPE
AC:Q7CH76
Organism:Yersinia pestis
Reign:Bacteria
TaxID:632
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:26.049
Number of residues:29
Including
Standard Amino Acids: 28
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors:
Metals: MN

Cavity properties

LigandabilityVolume (Å3)
0.8931161.000

% Hydrophobic% Polar
38.3761.63
According to VolSite

Ligand :
3n10_2 Structure
HET Code: CMP
Formula: C10H11N5O6P
Molecular weight: 328.198 g/mol
DrugBank ID: DB02527
Buried Surface Area:69 %
Polar Surface area: 167.48 Å2
Number of
H-Bond Acceptors: 10
H-Bond Donors: 2
Rings: 4
Aromatic rings: 2
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 1

Mass center Coordinates

XYZ
9.4470.094590940.6153


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
C2'CD2PHE- 53.720Hydrophobic
O1PNH1ARG- 632.88158.56H-Bond
(Protein Donor)
O1PNH2ARG- 633.29135.44H-Bond
(Protein Donor)
C5'CD1ILE- 743.480Hydrophobic
C4'SGCYS- 834.030Hydrophobic
C1'CBALA- 854.360Hydrophobic
O1PNH1ARG- 1133.21128.8H-Bond
(Protein Donor)
C1'SDMET- 1404.070Hydrophobic
O3'MN MN- 1832.40Metal Acceptor
O2'MN MN- 1832.490Metal Acceptor