scPDB - 2z2d entry

Protein Data Bank Entry:

PDB ID : 2z2d

Resolution : Å

Experimental Method : NMR

Deposition Date : 2007-05-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Macrophage metalloelastase
ID:	MMP12_HUMAN
AC:	P39900
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.4.24.65

Chains:

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

Ligand binding site composition:

B-Factor:	0.000
Number of residues:	30
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
1.120	577.125

% Hydrophobic	% Polar
54.39	45.61
According to VolSite

Ligand :

HET Code:	HSI
Formula:	C24H24ClO3
Molecular weight:	395.899 g/mol
DrugBank ID:	-
Buried Surface Area:	51.16 %
Polar Surface area:	57.2 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	0
Rings:	2
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
16.1171	19.5284	-22.5683

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
C56	CZ	PHE- 171	4.13	0	Hydrophobic	false
C40	CG2	ILE- 180	3.64	0	Hydrophobic	false
C9	CB	ILE- 180	3.98	0	Hydrophobic	false
O12	N	LEU- 181	2.59	150.26	H-Bond (Protein Donor)	false
C21	CB	LEU- 181	3.89	0	Hydrophobic	false
O12	N	ALA- 182	2.88	164.67	H-Bond (Protein Donor)	false
C26	CG	LEU- 214	4.48	0	Hydrophobic	false
C27	CD1	LEU- 214	3.52	0	Hydrophobic	false
C25	CD1	LEU- 214	3.3	0	Hydrophobic	false
C28	CG2	VAL- 235	3.87	0	Hydrophobic	false
C26	CE1	PHE- 237	3.76	0	Hydrophobic	false
C52	CB	PRO- 238	3.85	0	Hydrophobic	false
C44	CB	PRO- 238	4.17	0	Hydrophobic	false
C25	CD1	TYR- 240	4.21	0	Hydrophobic	false
C16	CB	TYR- 240	3.84	0	Hydrophobic	false
C33	CD	LYS- 241	3.8	0	Hydrophobic	false
C35	CB	LYS- 241	4.06	0	Hydrophobic	false
CL1	CG1	VAL- 243	3.75	0	Hydrophobic	false
C32	CG1	VAL- 243	3.35	0	Hydrophobic	false