scPDB - 2oy2 entry

Protein Data Bank Entry:

PDB ID : 2oy2

Resolution :1.500 Å

Experimental Method : X-ray

Deposition Date : 2007-02-21

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Neutrophil collagenase
ID:	MMP8_HUMAN
AC:	P22894
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.4.24.34

Chains:

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

Ligand binding site composition:

B-Factor:	6.188
Number of residues:	24
Including
Standard Amino Acids:	22
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.089	270.000

% Hydrophobic	% Polar
40.00	60.00
According to VolSite

Ligand :

HET Code:	ILE_ALA_GLY
Formula:	C11H21N3O4
Molecular weight:	259.302 g/mol
DrugBank ID:	-
Buried Surface Area:	53.27 %
Polar Surface area:	125.97 Å2

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

Mass center Coordinates

X	Y	Z
-12.5527	-0.126889	5.7115

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
N	O	GLY- 158	2.83	167.02	H-Bond (Ligand Donor)	false
O	N	LEU- 160	2.8	170.12	H-Bond (Protein Donor)	false
CG2	CD1	LEU- 160	3.77	0	Hydrophobic	false
N	O	ALA- 161	3.02	129.44	H-Bond (Ligand Donor)	false
CG2	CG1	VAL- 194	3.66	0	Hydrophobic	false
CD1	CB	HIS- 197	4.01	0	Hydrophobic	false
N	OE1	GLU- 198	3.88	0	Ionic (Ligand Cationic)	false
N	OE2	GLU- 198	2.66	0	Ionic (Ligand Cationic)	false
N	OE2	GLU- 198	2.66	161.59	H-Bond (Ligand Donor)	false
N	O	PRO- 217	3.32	151.91	H-Bond (Ligand Donor)	false
O	N	TYR- 219	2.8	173.29	H-Bond (Protein Donor)	false
CD1	CB	TYR- 219	3.89	0	Hydrophobic	false
N	O	HOH- 1059	2.66	135.57	H-Bond (Ligand Donor)	false