scPDB - 2ovz entry

Protein Data Bank Entry:

PDB ID : 2ovz

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2007-02-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Matrix metalloproteinase-9
ID:	MMP9_HUMAN
AC:	P14780
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.4.24.35

Chains:

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

Ligand binding site composition:

B-Factor:	26.716
Number of residues:	29
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.857	627.750

% Hydrophobic	% Polar
41.94	58.06
According to VolSite

Ligand :

HET Code:	5MR
Formula:	C30H28N4O5P
Molecular weight:	555.541 g/mol
DrugBank ID:	-
Buried Surface Area:	54.55 %
Polar Surface area:	163.95 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	3
Rings:	5
Aromatic rings:	5
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
70.7828	16.5237	54.0259

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
NAA	O	GLY- 186	3.35	163.23	H-Bond (Ligand Donor)	false
CAJ	CD1	LEU- 187	4.49	0	Hydrophobic	false
CZ3	CB	LEU- 187	3.36	0	Hydrophobic	false
CH2	CD1	LEU- 187	3.63	0	Hydrophobic	false
OAC	N	LEU- 188	2.84	161.55	H-Bond (Protein Donor)	false
CAP	CB	HIS- 190	3.57	0	Hydrophobic	false
DuAr	DuAr	HIS- 401	3.88	0	Aromatic Face/Face	false
CBE	CB	HIS- 401	4.1	0	Hydrophobic	false
OAD	NE2	GLN- 402	2.75	162.75	H-Bond (Protein Donor)	false
CAH	CD1	LEU- 418	4.09	0	Hydrophobic	false
CAI	CB	TYR- 420	4.2	0	Hydrophobic	false
N	O	PRO- 421	3.28	151.44	H-Bond (Ligand Donor)	false
O	N	TYR- 423	2.52	177.13	H-Bond (Protein Donor)	false
CBE	CB	TYR- 423	4.03	0	Hydrophobic	false
CAF	CG	ARG- 424	4.12	0	Hydrophobic	false
OAE	ZN	ZN- 444	1.81	0	Metal Acceptor	false