scPDB - 4ypa entry

Protein Data Bank Entry:

PDB ID : 4ypa

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2015-03-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Histone-lysine N-methyltransferase ASH1L
ID:	ASH1L_HUMAN
AC:	Q9NR48
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.1.1.43

Chains:

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

Ligand binding site composition:

B-Factor:	27.843
Number of residues:	31
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.369	519.750

% Hydrophobic	% Polar
30.52	69.48
According to VolSite

Ligand :

HET Code:	SAM
Formula:	C15H23N6O5S
Molecular weight:	399.445 g/mol
DrugBank ID:	DB00118
Buried Surface Area:	76.15 %
Polar Surface area:	189.77 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	2
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
-7.88359	9.87193	-10.8548

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
N	O	TRP- 2152	2.87	163.66	H-Bond (Ligand Donor)	false
OXT	N	TRP- 2152	2.98	169.03	H-Bond (Protein Donor)	false
C4'	CB	ASP- 2192	4.14	0	Hydrophobic	false
O2'	OD1	ASP- 2192	2.79	161.57	H-Bond (Ligand Donor)	false
O3'	N	HIS- 2193	3.22	138.63	H-Bond (Protein Donor)	false
O	OH	TYR- 2194	2.61	143.89	H-Bond (Protein Donor)	false
SD	CE1	TYR- 2194	3.52	0	Hydrophobic	false
CE	CD1	TYR- 2194	3.77	0	Hydrophobic	false
CB	CE1	TYR- 2194	4.27	0	Hydrophobic	false
CB	CD1	PHE- 2215	4.34	0	Hydrophobic	false
N	OD1	ASN- 2217	2.64	136.12	H-Bond (Ligand Donor)	false
N7	N	HIS- 2218	2.97	160.55	H-Bond (Protein Donor)	false
N6	O	HIS- 2218	2.79	146.44	H-Bond (Ligand Donor)	false
CE	CZ	TYR- 2255	3.91	0	Hydrophobic	false
C5'	CE1	TYR- 2255	3.61	0	Hydrophobic	false
C3'	CE1	TYR- 2255	4.48	0	Hydrophobic	false
O3'	OE1	GLN- 2266	2.83	162.48	H-Bond (Ligand Donor)	false
O3'	NE2	GLN- 2266	3.48	127.73	H-Bond (Protein Donor)	false
O2'	NE2	GLN- 2266	2.79	125.87	H-Bond (Protein Donor)	false
N1	N	LYS- 2269	2.91	137.68	H-Bond (Protein Donor)	false