scPDB - 1kyz entry

Protein Data Bank Entry:

PDB ID : 1kyz

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2002-02-06

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Caffeic acid 3-O-methyltransferase
ID:	COMT1_MEDSA
AC:	P28002
Organism:	Medicago sativa
Reign:	Eukaryota
TaxID:	3879
EC Number:	2.1.1.68

Chains:

Chain Name:	Percentage of Residues within binding site
A	5 %
E	95 %

Ligand binding site composition:

B-Factor:	25.688
Number of residues:	23
Including
Standard Amino Acids:	22
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.051	1613.250

% Hydrophobic	% Polar
55.86	44.14
According to VolSite

Ligand :

HET Code:	FER
Formula:	C10H9O4
Molecular weight:	193.176 g/mol
DrugBank ID:	DB07767
Buried Surface Area:	48.9 %
Polar Surface area:	69.59 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	1
Rings:	1
Aromatic rings:	1
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	3

Mass center Coordinates

X	Y	Z
30.5811	-4.6655	8.19336

Binding mode :

What is Poseview ?

2D View
3D View

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
O1	ND2	ASN- 131	3.12	170.1	H-Bond (Protein Donor)	false
C10	CD2	LEU- 136	3.46	0	Hydrophobic	false
C10	CB	ALA- 162	4.14	0	Hydrophobic	false
C4	CB	ALA- 162	4.13	0	Hydrophobic	false
C10	CZ	PHE- 172	3.85	0	Hydrophobic	false
C10	CE1	PHE- 176	4.02	0	Hydrophobic	false
C2	CE1	PHE- 176	3.49	0	Hydrophobic	false
C6	SD	MET- 320	3.96	0	Hydrophobic	false
C1	CE	MET- 320	3.98	0	Hydrophobic	false
C5	CE	MET- 320	3.48	0	Hydrophobic	false