scPDB - 2dw0 entry

Protein Data Bank Entry:

PDB ID : 2dw0

Resolution :2.150 Å

Experimental Method : X-ray

Deposition Date : 2006-08-02

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Zinc metalloproteinase-disintegrin-like VAP2B
ID:	VM3VB_CROAT
AC:	Q90282
Organism:	Crotalus atrox
Reign:	Eukaryota
TaxID:	8730
EC Number:	3.4.24

Chains:

Chain Name:	Percentage of Residues within binding site
A	4 %
B	96 %

Ligand binding site composition:

B-Factor:	14.779
Number of residues:	23
Including
Standard Amino Acids:	22
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.447	307.125

% Hydrophobic	% Polar
52.75	47.25
According to VolSite

Ligand :

HET Code:	GM6
Formula:	C20H28N4O4
Molecular weight:	388.461 g/mol
DrugBank ID:	DB02255
Buried Surface Area:	57.24 %
Polar Surface area:	123.32 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	5
Rings:	2
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
-8.48382	38.9941	6.38661

Binding mode :

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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
CAX	CB	ARG- 297	3.72	0	Hydrophobic	false
CAC	CG1	VAL- 298	3.89	0	Hydrophobic	false
OAL	N	ILE- 299	2.76	149.35	H-Bond (Protein Donor)	false
CAJ	CD1	ILE- 299	3.89	0	Hydrophobic	false
CAH	CG1	ILE- 299	3.92	0	Hydrophobic	false
NAF	O	GLY- 300	3.09	150.62	H-Bond (Ligand Donor)	false
CAJ	CG1	ILE- 330	3.95	0	Hydrophobic	false
CAJ	CB	HIS- 333	4.31	0	Hydrophobic	false
OAG	OE1	GLU- 334	2.63	158.23	H-Bond (Protein Donor)	false
NAM	O	PRO- 359	3.27	159.85	H-Bond (Ligand Donor)	false
CAO	CB	GLU- 360	3.94	0	Hydrophobic	false
OAZ	N	ILE- 361	2.92	161.53	H-Bond (Protein Donor)	false
CAI	CB	ILE- 361	4.43	0	Hydrophobic	false
OAG	ZN	ZN- 700	2.3	0	Metal Acceptor	false
OAE	ZN	ZN- 700	2.06	0	Metal Acceptor	false