scPDB - 4i03 entry

Protein Data Bank Entry:

PDB ID : 4i03

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2012-11-16

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:	22.675
Number of residues:	33
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.612	499.500

% Hydrophobic	% Polar
43.24	56.76
According to VolSite

Ligand :

HET Code:	L88
Formula:	C58H64N4O11S2
Molecular weight:	1057.279 g/mol
DrugBank ID:	-
Buried Surface Area:	32.29 %
Polar Surface area:	280.82 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	4
Rings:	6
Aromatic rings:	6
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	34

Mass center Coordinates

X	Y	Z
13.5217	-6.64345	24.5138

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
C8	CG2	ILE- 180	4.08	0	Hydrophobic	false
C54	CG1	ILE- 180	3.44	0	Hydrophobic	false
O2	N	LEU- 181	2.71	156.8	H-Bond (Protein Donor)	false
C12	CD1	LEU- 181	4.22	0	Hydrophobic	false
C28	CD1	LEU- 181	4.41	0	Hydrophobic	false
O2	N	ALA- 182	3.25	164.31	H-Bond (Protein Donor)	false
C9	CB	HIS- 183	4.2	0	Hydrophobic	false
S7	CB	LEU- 214	3.78	0	Hydrophobic	false
C28	CG2	THR- 215	4.08	0	Hydrophobic	false
DuAr	DuAr	HIS- 218	3.58	0	Aromatic Face/Face	false
C15	CB	HIS- 218	3.74	0	Hydrophobic	false
C21	CG2	VAL- 235	4.34	0	Hydrophobic	false
C25	CB	PHE- 237	4.17	0	Hydrophobic	false
C69	CG2	THR- 239	4.45	0	Hydrophobic	false
C15	CB	TYR- 240	4.08	0	Hydrophobic	false
C21	CB	LYS- 241	4.08	0	Hydrophobic	false
C26	CD	LYS- 241	3.6	0	Hydrophobic	false
C23	CG1	VAL- 243	4.26	0	Hydrophobic	false
O4	ZN	ZN- 301	2.39	0	Metal Acceptor	false
O4E	ZN	ZN- 301	2.43	0	Metal Acceptor	false