scPDB - 3ljt entry

Protein Data Bank Entry:

PDB ID : 3ljt

Resolution :1.600 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:	A disintegrin and metalloproteinase with thrombospondin motifs 5
ID:	ATS5_HUMAN
AC:	Q9UNA0
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:	12.245
Number of residues:	28
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
1.163	675.000

% Hydrophobic	% Polar
47.50	52.50
According to VolSite

Ligand :

HET Code:	LA3
Formula:	C27H26N2O6
Molecular weight:	474.505 g/mol
DrugBank ID:	-
Buried Surface Area:	59.79 %
Polar Surface area:	117.12 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	4
Rings:	5
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
12.9543	3.1294	27.3562

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
C32	CB	ASP- 377	3.64	0	Hydrophobic	false
C35	CB	ASP- 377	3.49	0	Hydrophobic	false
C19	CG2	THR- 378	4.38	0	Hydrophobic	false
C4	CD1	LEU- 379	4.41	0	Hydrophobic	false
C28	CD1	LEU- 379	4.04	0	Hydrophobic	false
O24	N	LEU- 379	2.72	136.01	H-Bond (Protein Donor)	false
N22	O	GLY- 380	2.91	161.99	H-Bond (Ligand Donor)	false
C11	CB	HIS- 403	4.03	0	Hydrophobic	false
C16	CD2	PHE- 406	3.64	0	Hydrophobic	false
C11	CB	PHE- 406	3.77	0	Hydrophobic	false
C9	CB	PHE- 406	3.63	0	Hydrophobic	false
C1	CB	THR- 407	4.05	0	Hydrophobic	false
C4	CG2	THR- 407	3.82	0	Hydrophobic	false
C16	CD2	LEU- 438	3.97	0	Hydrophobic	false
C13	CD2	LEU- 438	3.89	0	Hydrophobic	false
N25	O	SER- 441	3.03	172.94	H-Bond (Ligand Donor)	false
C32	CG2	ILE- 442	4.02	0	Hydrophobic	false
C31	CG2	ILE- 442	3.74	0	Hydrophobic	false
C3	CD2	LEU- 443	4.46	0	Hydrophobic	false
C9	CB	LEU- 443	4.5	0	Hydrophobic	false
C28	CD2	LEU- 443	3.88	0	Hydrophobic	false
C30	CG	LEU- 443	3.97	0	Hydrophobic	false
C7	CB	LEU- 443	4.01	0	Hydrophobic	false
C11	CD2	LEU- 443	3.49	0	Hydrophobic	false
O29	N	LEU- 443	3.26	143.09	H-Bond (Protein Donor)	false
C16	CD1	ILE- 446	4.2	0	Hydrophobic	false
C10	CD1	ILE- 446	3.3	0	Hydrophobic	false
C13	CD1	ILE- 446	3.35	0	Hydrophobic	false
O21	ZN	ZN- 901	2.21	0	Metal Acceptor	false
O23	ZN	ZN- 901	2.19	0	Metal Acceptor	false