scPDB - 2vd7 entry

Protein Data Bank Entry:

PDB ID : 2vd7

Resolution :2.250 Å

Experimental Method : X-ray

Deposition Date : 2007-10-01

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 4A
ID:	KDM4A_HUMAN
AC:	O75164
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	1.14.11

Chains:

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

Ligand binding site composition:

B-Factor:	39.895
Number of residues:	22
Including
Standard Amino Acids:	22
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.467	847.125

% Hydrophobic	% Polar
35.46	64.54
According to VolSite

Ligand :

HET Code:	PD2
Formula:	C7H3NO4
Molecular weight:	165.103 g/mol
DrugBank ID:	-
Buried Surface Area:	70.14 %
Polar Surface area:	93.15 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	0
Rings:	1
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
8.02058	-55.4143	2.50983

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
O42	OH	TYR- 132	3.04	128.14	H-Bond (Protein Donor)	false
O41	OH	TYR- 132	2.5	132.26	H-Bond (Protein Donor)	false
C4	CB	PHE- 185	3.89	0	Hydrophobic	false
O42	NZ	LYS- 206	2.71	170.72	H-Bond (Protein Donor)	false
O42	NZ	LYS- 206	2.71	0	Ionic (Protein Cationic)	false
O21	NZ	LYS- 241	3.41	128.5	H-Bond (Protein Donor)	false
O22	NZ	LYS- 241	2.86	177.23	H-Bond (Protein Donor)	false
O21	NZ	LYS- 241	3.41	0	Ionic (Protein Cationic)	false
O22	NZ	LYS- 241	2.86	0	Ionic (Protein Cationic)	false