scPDB - 2jsd entry

Protein Data Bank Entry:

PDB ID : 2jsd

Resolution : Å

Experimental Method : NMR

Deposition Date : 2007-07-03

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Matrix metalloproteinase-20
ID:	MMP20_HUMAN
AC:	O60882
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.4.24

Chains:

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

Ligand binding site composition:

B-Factor:	0.000
Number of residues:	24
Including
Standard Amino Acids:	23
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.147	249.750

% Hydrophobic	% Polar
41.89	58.11
According to VolSite

Ligand :

HET Code:	NGH
Formula:	C13H20N2O5S
Molecular weight:	316.373 g/mol
DrugBank ID:	DB08271
Buried Surface Area:	66.68 %
Polar Surface area:	104.32 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	2
Rings:	1
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
6.32567	-4.79305	4.79057

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
C10	CG2	THR- 188	4.28	0	Hydrophobic	false
C5	CB	LEU- 189	4.07	0	Hydrophobic	false
C5	CB	ALA- 190	4.48	0	Hydrophobic	false
O2	N	ALA- 190	3.04	164.06	H-Bond (Protein Donor)	false
C7	CG2	THR- 222	4.48	0	Hydrophobic	false
C4	CG1	VAL- 223	3.98	0	Hydrophobic	false
C3	CB	HIS- 226	4.06	0	Hydrophobic	false
C7	CB	HIS- 226	4.06	0	Hydrophobic	false
C14	CB	PRO- 246	4.09	0	Hydrophobic	false
C13	CB	PRO- 246	3.88	0	Hydrophobic	false
C7	CD1	TYR- 248	4.22	0	Hydrophobic	false
C2	CB	TYR- 248	4.25	0	Hydrophobic	false
O4	ZN	ZN- 276	2.19	0	Metal Acceptor	false
O5	ZN	ZN- 276	2.16	0	Metal Acceptor	false