scPDB - 2ddy entry

Protein Data Bank Entry:

PDB ID : 2ddy

Resolution : Å

Experimental Method : NMR

Deposition Date : 2006-02-06

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Matrilysin
ID:	MMP7_HUMAN
AC:	P09237
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.4.24.23

Chains:

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

Ligand binding site composition:

B-Factor:	0.000
Number of residues:	27
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.174	283.500

% Hydrophobic	% Polar
45.24	54.76
According to VolSite

Ligand :

HET Code:	MDW
Formula:	C18H20N2O7S
Molecular weight:	408.426 g/mol
DrugBank ID:	DB08170
Buried Surface Area:	53.26 %
Polar Surface area:	133.78 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
6.45657	1.85614	7.31732

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
C5	CG2	THR- 81	4.13	0	Hydrophobic	false
O40	N	LEU- 82	2.75	145.13	H-Bond (Protein Donor)	false
C26	CD2	LEU- 82	4.44	0	Hydrophobic	false
C20	CB	LEU- 82	4.24	0	Hydrophobic	false
C24	CD1	LEU- 82	3.52	0	Hydrophobic	false
N16	O	ALA- 83	3.45	156.3	H-Bond (Ligand Donor)	false
O40	N	ALA- 83	3.16	176.54	H-Bond (Protein Donor)	false
C20	CB	ALA- 83	4.19	0	Hydrophobic	false
C13	CB	HIS- 84	4.41	0	Hydrophobic	false
C26	CZ3	TRP- 104	4	0	Hydrophobic	false
C26	CG2	ILE- 112	3.21	0	Hydrophobic	false
C26	CD2	TYR- 116	3.96	0	Hydrophobic	false
C26	CB	ALA- 117	3.5	0	Hydrophobic	false
C22	CB	ALA- 117	4.44	0	Hydrophobic	false
O17	OE1	GLU- 121	2.61	139.38	H-Bond (Protein Donor)	false
C10	CB	PRO- 140	3.99	0	Hydrophobic	false
C26	CE2	TYR- 142	3.51	0	Hydrophobic	false
O15	ZN	ZN- 177	2.07	0	Metal Acceptor	false
O17	ZN	ZN- 177	2.5	0	Metal Acceptor	false