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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:

2y1x

2.400 Å

X-ray

2010-12-10

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Histone-arginine methyltransferase CARM1
ID:CARM1_HUMAN
AC:Q86X55
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:24.753
Number of residues:33
Including
Standard Amino Acids: 29
Non Standard Amino Acids: 2
Water Molecules: 2
Cofactors:
Metals: CL

Cavity properties

LigandabilityVolume (Å3)
0.717729.000

% Hydrophobic% Polar
43.5256.48
According to VolSite

Ligand :
2y1x_2 Structure
HET Code: 845
Formula: C24H23F3N7O2
Molecular weight: 498.480 g/mol
DrugBank ID: -
Buried Surface Area:62.47 %
Polar Surface area: 121.42 Å2
Number of
H-Bond Acceptors: 6
H-Bond Donors: 5
Rings: 5
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 6

Mass center Coordinates

XYZ
29.5543-19.2566-22.5447


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
C23CZTYR- 1544.360Hydrophobic
C7CBASN- 1624.210Hydrophobic
F17CBASN- 1623.460Hydrophobic
C7CGMET- 1634.30Hydrophobic
C9SDMET- 1633.790Hydrophobic
N22OE1GLU- 2582.850Ionic
(Ligand Cationic)
N22OE2GLU- 2582.760Ionic
(Ligand Cationic)
N22OGLU- 2582.55138.9H-Bond
(Ligand Donor)
N22OE2GLU- 2582.76139.25H-Bond
(Ligand Donor)
N22OMET- 2603.15140.46H-Bond
(Ligand Donor)
N14OE2GLU- 2672.69140.15H-Bond
(Ligand Donor)
C23SDMET- 2694.420Hydrophobic
O21NE2HIS- 4152.79163.63H-Bond
(Protein Donor)
F18CBHIS- 4153.840Hydrophobic
F18CE1TYR- 4173.710Hydrophobic
C29CZPHE- 4753.490Hydrophobic
F16CE1TYR- 4774.490Hydrophobic
F18CZTYR- 4774.280Hydrophobic