scPDB - 3u78 entry

Protein Data Bank Entry:

PDB ID : 3u78

Resolution :2.690 Å

Experimental Method : X-ray

Deposition Date : 2011-10-13

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 7A
ID:	KDM7A_HUMAN
AC:	Q6ZMT4
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:	42.017
Number of residues:	29
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.569	793.125

% Hydrophobic	% Polar
37.87	62.13
According to VolSite

Ligand :

HET Code:	E67
Formula:	C31H50N7O2
Molecular weight:	552.774 g/mol
DrugBank ID:	-
Buried Surface Area:	37.85 %
Polar Surface area:	104.82 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	5
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	3
Rule of Five Violation:	1
Rotatable Bonds:	16

Mass center Coordinates

X	Y	Z
-43.8225	23.4642	18.7896

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
NAN	O	GLN- 200	3.42	126.69	H-Bond (Ligand Donor)	false
CBD	CD1	ILE- 226	4.13	0	Hydrophobic	false
CAM	CG2	THR- 279	3.8	0	Hydrophobic	false
CBB	CG2	THR- 279	3.89	0	Hydrophobic	false
CAM	CB	ASP- 280	4.47	0	Hydrophobic	false
CBB	CB	HIS- 282	4.25	0	Hydrophobic	false
CBF	CD2	PHE- 285	4.27	0	Hydrophobic	false
CAW	CG	PRO- 391	4.16	0	Hydrophobic	false
CBF	CB	ASP- 392	4.44	0	Hydrophobic	false