scPDB - 1zga entry

Protein Data Bank Entry:

PDB ID : 1zga

Resolution :2.350 Å

Experimental Method : X-ray

Deposition Date : 2005-04-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Isoflavone 4'-O-methyltransferase
ID:	I4OMT_MEDTR
AC:	Q29U70
Organism:	Medicago truncatula
Reign:	Eukaryota
TaxID:	3880
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	36.002
Number of residues:	26
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.298	1461.375

% Hydrophobic	% Polar
65.59	34.41
According to VolSite

Ligand :

HET Code:	HMK
Formula:	C16H12O6
Molecular weight:	300.263 g/mol
DrugBank ID:	-
Buried Surface Area:	54.47 %
Polar Surface area:	77.38 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	2
Rings:	5
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	0

Mass center Coordinates

X	Y	Z
100.795	75.5155	32.7152

Binding mode :

What is Poseview ?

2D View
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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

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
C16	CZ	PHE- 159	3.44	0	Hydrophobic	false
C13	CE	MET- 174	4.43	0	Hydrophobic	false
C16	CE	MET- 174	3.51	0	Hydrophobic	false
C13	CB	PHE- 175	4.45	0	Hydrophobic	false
C16	CD2	PHE- 175	4.17	0	Hydrophobic	false
C12	CB	ALA- 178	3.8	0	Hydrophobic	false
C8	CB	ASP- 182	3.73	0	Hydrophobic	false
O6	OD1	ASP- 182	3.11	132.14	H-Bond (Ligand Donor)	false
C1	CE2	TYR- 318	4.27	0	Hydrophobic	false
C1	CG1	VAL- 321	4.2	0	Hydrophobic	false
C1	CE	MET- 322	3.47	0	Hydrophobic	false
C1	CE	MET- 325	4.4	0	Hydrophobic	false
C15	CE	MET- 325	3.33	0	Hydrophobic	false