scPDB - 3kme entry

Protein Data Bank Entry:

PDB ID : 3kme

Resolution :1.850 Å

Experimental Method : X-ray

Deposition Date : 2009-11-10

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Disintegrin and metalloproteinase domain-containing protein 17
ID:	ADA17_HUMAN
AC:	P78536
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.4.24.86

Chains:

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

Ligand binding site composition:

B-Factor:	29.298
Number of residues:	27
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.339	455.625

% Hydrophobic	% Polar
40.00	60.00
According to VolSite

Ligand :

HET Code:	INN
Formula:	C19H38N5O5
Molecular weight:	416.536 g/mol
DrugBank ID:	-
Buried Surface Area:	52.55 %
Polar Surface area:	164.27 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	6
Rings:	0
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
6.16324	5.49917	24.8714

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
O	ZN	ZN- 1	2.04	0	Metal Acceptor	false
O4	ZN	ZN- 1	2.22	0	Metal Acceptor	false
N2	O	GLY- 346	2.69	175.33	H-Bond (Ligand Donor)	false
C8	CB	THR- 347	4.46	0	Hydrophobic	false
O1	N	LEU- 348	2.77	150.73	H-Bond (Protein Donor)	false
C3	CD1	LEU- 348	4.21	0	Hydrophobic	false
C12	CD1	LEU- 348	3.74	0	Hydrophobic	false
N	O	GLY- 349	3.04	154.02	H-Bond (Ligand Donor)	false
O3	ND2	ASN- 389	3.36	148.17	H-Bond (Protein Donor)	false
N4	OH	TYR- 390	3.44	145.57	H-Bond (Ligand Donor)	false
C3	CG2	VAL- 402	3.96	0	Hydrophobic	false
C3	CB	HIS- 405	4.31	0	Hydrophobic	false
O4	OE1	GLU- 406	2.53	151.81	H-Bond (Protein Donor)	false
N1	O	PRO- 437	3.4	169.71	H-Bond (Ligand Donor)	false
C9	CD1	ILE- 438	3.6	0	Hydrophobic	false
O2	N	ALA- 439	2.75	173.43	H-Bond (Protein Donor)	false
C12	CB	ALA- 439	3.54	0	Hydrophobic	false
C1	CB	ALA- 439	4.08	0	Hydrophobic	false