scPDB - 3lgp entry

Protein Data Bank Entry:

PDB ID : 3lgp

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2010-01-21

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	8.700	8.700	8.700	0.000	8.700	1

List of CHEMBLId :

CHEMBL1230339

Binding Site :

Uniprot Annotation

Name:	Disintegrin and metalloproteinase domain-containing protein 17
ID:	ADA17_HUMAN
AC:	P78536
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.4.24.86

Chains:

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

Ligand binding site composition:

B-Factor:	33.197
Number of residues:	41
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.602	486.000

% Hydrophobic	% Polar
43.75	56.25
According to VolSite

Ligand :

HET Code:	50X
Formula:	C28H26ClF3N4O4S
Molecular weight:	607.044 g/mol
DrugBank ID:	-
Buried Surface Area:	65.17 %
Polar Surface area:	135.93 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	3
Rings:	5
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
49.836	31.5588	41.869

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
O26	ZN	ZN- 2	2.06	0	Metal Acceptor	false
O28	ZN	ZN- 2	2.36	0	Metal Acceptor	false
O29	ZN	ZN- 2	2.52	0	Metal Acceptor	false
C4	CG1	VAL- 314	4.08	0	Hydrophobic	false
C4	CG2	THR- 347	4.41	0	Hydrophobic	false
C10	CD1	LEU- 348	4.1	0	Hydrophobic	false
O24	N	LEU- 348	2.96	169.18	H-Bond (Protein Donor)	false
O24	N	GLY- 349	3.41	151.05	H-Bond (Protein Donor)	false
C21	CD1	LEU- 350	4.41	0	Hydrophobic	false
C4	CD1	LEU- 350	3.81	0	Hydrophobic	false
C10	CB	GLU- 398	3.63	0	Hydrophobic	false
C9	CG	GLU- 398	3.51	0	Hydrophobic	false
C6	CD1	LEU- 401	3.8	0	Hydrophobic	false
C8	CD1	LEU- 401	4.48	0	Hydrophobic	false
C30	CB	LEU- 401	3.99	0	Hydrophobic	false
C11	CB	LEU- 401	3.44	0	Hydrophobic	false
S16	CG2	VAL- 402	4.29	0	Hydrophobic	false
C10	CG2	VAL- 402	4.03	0	Hydrophobic	false
S16	CB	HIS- 405	3.54	0	Hydrophobic	false
N25	NE2	HIS- 405	3.35	162.69	H-Bond (Ligand Donor)	false
DuAr	DuAr	HIS- 405	3.8	0	Aromatic Face/Face	false
O26	OE2	GLU- 406	2.56	174.55	H-Bond (Ligand Donor)	false
O26	OE1	GLU- 406	3.17	121.71	H-Bond (Ligand Donor)	false
F32	CB	LYS- 432	3.76	0	Hydrophobic	false
C30	CG2	VAL- 434	4.12	0	Hydrophobic	false
F33	CB	TYR- 436	3.28	0	Hydrophobic	false
O28	O	PRO- 437	3.03	162.71	H-Bond (Ligand Donor)	false
CL41	CB	PRO- 437	4.07	0	Hydrophobic	false
CL41	CG1	ILE- 438	4.16	0	Hydrophobic	false
S16	CB	ALA- 439	4.33	0	Hydrophobic	false
C10	CB	ALA- 439	3.49	0	Hydrophobic	false
F32	CG2	VAL- 440	4.03	0	Hydrophobic	false
N14	N	SER- 441	3.2	137.28	H-Bond (Protein Donor)	false
F32	CB	SER- 441	3.81	0	Hydrophobic	false
F34	CB	ASN- 447	3.38	0	Hydrophobic	false