scPDB - 3ljg entry

Protein Data Bank Entry:

PDB ID : 3ljg

Resolution :1.310 Å

Experimental Method : X-ray

Deposition Date : 2010-01-26

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:	12.145
Number of residues:	33
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.860	583.875

% Hydrophobic	% Polar
38.73	61.27
According to VolSite

Ligand :

HET Code:	EEF
Formula:	C25H27N3O7
Molecular weight:	481.498 g/mol
DrugBank ID:	-
Buried Surface Area:	49.14 %
Polar Surface area:	181.55 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	3
Rings:	2
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	14

Mass center Coordinates

X	Y	Z
6.47909	26.8239	6.64994

Binding mode :

What is Poseview ?

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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
N2	O	GLY- 179	2.82	151.44	H-Bond (Ligand Donor)	false
O2	N	LEU- 181	2.82	159.93	H-Bond (Protein Donor)	false
C12	CD2	LEU- 181	4.29	0	Hydrophobic	false
C20	CB	LEU- 214	3.96	0	Hydrophobic	false
C21	CD1	LEU- 214	3.99	0	Hydrophobic	false
C15	CG2	THR- 215	3.98	0	Hydrophobic	false
DuAr	DuAr	HIS- 218	3.86	0	Aromatic Face/Face	false
C15	CB	HIS- 218	3.78	0	Hydrophobic	false
C23	CG2	VAL- 235	4.05	0	Hydrophobic	false
N1	O	PRO- 238	2.98	172.82	H-Bond (Ligand Donor)	false
C4	CG2	THR- 239	4.46	0	Hydrophobic	false
O1	N	TYR- 240	2.87	165.56	H-Bond (Protein Donor)	false
N3	O	TYR- 240	3.21	131.85	H-Bond (Ligand Donor)	false
C16	CB	TYR- 240	3.9	0	Hydrophobic	false
C27	CG2	VAL- 243	4.2	0	Hydrophobic	false