scPDB - 5icf entry

Protein Data Bank Entry:

PDB ID : 5icf

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2016-02-23

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	(S)-norcoclaurine 6-O-methyltransferase
ID:	Q5C9L7_THLFG
AC:	Q5C9L7
Organism:	Thalictrum flavum subsp. glaucum
Reign:	Eukaryota
TaxID:	150095
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	11.796
Number of residues:	41
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	6
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.670	435.375

% Hydrophobic	% Polar
53.49	46.51
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	74.49 %
Polar Surface area:	212.38 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
9.54623	23.1251	-2.02773

Binding mode :

What is Poseview ?

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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
C5'	CH2	TRP- 149	3.89	0	Hydrophobic	false
C2'	CZ3	TRP- 149	3.67	0	Hydrophobic	false
SD	CZ	PHE- 162	3.89	0	Hydrophobic	false
C3'	CE2	PHE- 162	4.32	0	Hydrophobic	false
CB	CB	MET- 166	4.29	0	Hydrophobic	false
CG	CE	MET- 166	3.71	0	Hydrophobic	false
SD	CG	MET- 166	3.96	0	Hydrophobic	false
N	O	GLY- 195	2.82	162.76	H-Bond (Ligand Donor)	false
O3'	OD1	ASP- 218	3.47	126.63	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 218	2.68	163.3	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 218	2.64	150.02	H-Bond (Ligand Donor)	false
C2'	CD1	LEU- 219	4.46	0	Hydrophobic	false
N6	OD1	ASP- 238	2.79	166.86	H-Bond (Ligand Donor)	false
N1	N	MET- 239	2.85	172.29	H-Bond (Protein Donor)	false
N	O	LYS- 252	2.75	158.37	H-Bond (Ligand Donor)	false
O	NZ	LYS- 252	3.42	0	Ionic (Protein Cationic)	false
OXT	NZ	LYS- 252	2.72	0	Ionic (Protein Cationic)	false
OXT	NZ	LYS- 252	2.72	150.1	H-Bond (Protein Donor)	false
CG	CB	CYS- 253	3.84	0	Hydrophobic	false
CG	CD1	ILE- 254	4.07	0	Hydrophobic	false
C4'	CD1	ILE- 254	3.67	0	Hydrophobic	false
O4'	O	HOH- 622	2.94	150.68	H-Bond (Protein Donor)	false