scPDB - 4ask entry

Protein Data Bank Entry:

PDB ID : 4ask

Resolution :1.860 Å

Experimental Method : X-ray

Deposition Date : 2012-05-01

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Lysine-specific demethylase 6B
ID:	KDM6B_HUMAN
AC:	O15054
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	1.14.11

Chains:

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

Ligand binding site composition:

B-Factor:	19.010
Number of residues:	33
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.563	860.625

% Hydrophobic	% Polar
25.10	74.90
According to VolSite

Ligand :

HET Code:	K0I
Formula:	C22H22N5O2
Molecular weight:	388.442 g/mol
DrugBank ID:	-
Buried Surface Area:	63.1 %
Polar Surface area:	94.07 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	1
Rings:	4
Aromatic rings:	3
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
49.216	14.6192	-18.1009

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
C19	CG	ARG- 1246	3.78	0	Hydrophobic	false
C18	CD	ARG- 1246	3.62	0	Hydrophobic	false
C18	CB	SER- 1270	4.27	0	Hydrophobic	false
C21	CE2	PHE- 1328	3.85	0	Hydrophobic	false
C22	CG2	THR- 1330	3.53	0	Hydrophobic	false
C2	CE2	TYR- 1379	4.25	0	Hydrophobic	false
C3	CZ	TYR- 1379	3.71	0	Hydrophobic	false
C22	CE1	TYR- 1379	4.16	0	Hydrophobic	false
O2	NZ	LYS- 1381	2.69	133.79	H-Bond (Protein Donor)	false
O1	NZ	LYS- 1381	3.02	157.32	H-Bond (Protein Donor)	false
O2	NZ	LYS- 1381	2.69	0	Ionic (Protein Cationic)	false
O1	NZ	LYS- 1381	3.02	0	Ionic (Protein Cationic)	false
O2	OG1	THR- 1387	2.64	148.8	H-Bond (Protein Donor)	false
C5	CG2	THR- 1387	3.93	0	Hydrophobic	false
C21	CG2	THR- 1387	4.43	0	Hydrophobic	false
C3	CG2	THR- 1387	3.65	0	Hydrophobic	false
C18	CG	PRO- 1388	3.8	0	Hydrophobic	false
O1	ND2	ASN- 1400	2.9	155.24	H-Bond (Protein Donor)	false