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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:

4zz6

2.000 Å

X-ray

2015-05-22

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Ribosome inactivating protein
ID:D9J2T9_MOMBA
AC:D9J2T9
Organism:Momordica balsamina
Reign:Eukaryota
TaxID:3672
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:27.042
Number of residues:28
Including
Standard Amino Acids: 26
Non Standard Amino Acids: 0
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.187263.250

% Hydrophobic% Polar
42.3157.69
According to VolSite

Ligand :
4zz6_1 Structure
HET Code: CTP
Formula: C9H12N3O14P3
Molecular weight: 479.125 g/mol
DrugBank ID: DB02431
Buried Surface Area:59.95 %
Polar Surface area: 308.95 Å2
Number of
H-Bond Acceptors: 16
H-Bond Donors: 3
Rings: 2
Aromatic rings: 0
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 8

Mass center Coordinates

XYZ
-5.93155-21.2223-6.75497


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'CD2TYR- 703.810Hydrophobic
C5'CZTYR- 703.610Hydrophobic
C3'CE2TYR- 703.220Hydrophobic
O2NILE- 712.95164.8H-Bond
(Protein Donor)
N4OILE- 712.85140.19H-Bond
(Ligand Donor)
N4OE1GLU- 853.37152.42H-Bond
(Ligand Donor)
O1BND2ASN- 1102.54162.82H-Bond
(Protein Donor)
O2ANTYR- 1112.83161.86H-Bond
(Protein Donor)
O3ANTYR- 1112.93125.02H-Bond
(Protein Donor)
O1BNGLU- 1122.78150.43H-Bond
(Protein Donor)
O1GNH1ARG- 1223.44129.53H-Bond
(Protein Donor)
C1'CG2ILE- 1554.110Hydrophobic
O2'NH2ARG- 1633.5125.94H-Bond
(Protein Donor)
O2'NH1ARG- 1632.71159.6H-Bond
(Protein Donor)
O3'OHOH- 4232.64140.63H-Bond
(Ligand Donor)