scPDB - 5il2 entry

Protein Data Bank Entry:

PDB ID : 5il2

Resolution :1.610 Å

Experimental Method : X-ray

Deposition Date : 2016-03-04

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	N6-adenosine-methyltransferase 70 kDa subunit
ID:	MTA70_HUMAN
AC:	Q86U44
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	40.813
Number of residues:	33
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.062	995.625

% Hydrophobic	% Polar
44.07	55.93
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	65.36 %
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
30.4605	21.1841	27.3081

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
N6	OD2	ASP- 377	2.92	152.23	H-Bond (Ligand Donor)	false
N1	N	ILE- 378	2.92	169.01	H-Bond (Protein Donor)	false
N	OD2	ASP- 395	2.88	164.39	H-Bond (Ligand Donor)	false
N	OD2	ASP- 395	2.88	0	Ionic (Ligand Cationic)	false
CB	CB	ASP- 395	4.48	0	Hydrophobic	false
CB	CB	SER- 511	4.23	0	Hydrophobic	false
SD	CB	SER- 511	4.21	0	Hydrophobic	false
OXT	N	LYS- 513	3.11	149.07	H-Bond (Protein Donor)	false
N	OE2	GLU- 532	3.99	0	Ionic (Ligand Cationic)	false
C1'	CD1	PHE- 534	4.28	0	Hydrophobic	false
C5'	CB	PHE- 534	3.93	0	Hydrophobic	false
SD	CD	ARG- 536	4.36	0	Hydrophobic	false
C4'	CG	ARG- 536	4.44	0	Hydrophobic	false
C3'	CD	ARG- 536	4.11	0	Hydrophobic	false
CG	CG	ARG- 536	3.52	0	Hydrophobic	false
O	NE2	HIS- 538	2.67	171.72	H-Bond (Protein Donor)	false
OXT	NE2	HIS- 538	3.33	120.6	H-Bond (Protein Donor)	false
OXT	ND2	ASN- 539	3.09	157.06	H-Bond (Protein Donor)	false
O2'	OD1	ASN- 549	2.66	164.93	H-Bond (Ligand Donor)	false
N3	N	ASN- 549	3.08	135.39	H-Bond (Protein Donor)	false
O3'	OE1	GLN- 550	2.61	149.92	H-Bond (Ligand Donor)	false
O3'	O	HOH- 710	3.02	158.86	H-Bond (Protein Donor)	false
N	O	HOH- 727	2.82	153.73	H-Bond (Ligand Donor)	false