scPDB - 4cth entry

Protein Data Bank Entry:

PDB ID : 4cth

Resolution :2.150 Å

Experimental Method : X-ray

Deposition Date : 2014-03-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Neprilysin
ID:	NEP_HUMAN
AC:	P08473
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	31.159
Number of residues:	26
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.329	553.500

% Hydrophobic	% Polar
47.56	52.44
According to VolSite

Ligand :

HET Code:	RDF
Formula:	C23H32N3O10P
Molecular weight:	541.488 g/mol
DrugBank ID:	DB02557
Buried Surface Area:	55.54 %
Polar Surface area:	226.14 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	6
Rings:	3
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
-51.9896	-4.23784	-15.6794

Binding mode :

What is Poseview ?

2D View
3D View

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
CZ2	CB	PHE- 106	3.49	0	Hydrophobic	false
NE1	O	VAL- 541	2.85	161.73	H-Bond (Ligand Donor)	false
CZ2	CG1	VAL- 541	3.84	0	Hydrophobic	false
N1	OD1	ASN- 542	3.33	154.03	H-Bond (Ligand Donor)	false
OXT	ND2	ASN- 542	3	154.49	H-Bond (Protein Donor)	false
N	O	ALA- 543	3.06	145.3	H-Bond (Ligand Donor)	false
CB	CB	ALA- 543	4.3	0	Hydrophobic	false
C2	CE2	PHE- 544	3.81	0	Hydrophobic	false
C3	CD2	PHE- 544	3.93	0	Hydrophobic	false
CD2	CD1	ILE- 558	3.55	0	Hydrophobic	false
CD2	CE1	PHE- 563	4.33	0	Hydrophobic	false
CH2	CZ	PHE- 563	3.48	0	Hydrophobic	false
CD1	CG2	VAL- 580	3.95	0	Hydrophobic	false
CD2	CG2	VAL- 580	3.93	0	Hydrophobic	false
CD1	CB	HIS- 583	4.19	0	Hydrophobic	false
O1P	OE1	GLU- 584	2.69	157.95	H-Bond (Protein Donor)	false
N	OE2	GLU- 584	3.48	122.4	H-Bond (Ligand Donor)	false
CB1	CZ3	TRP- 693	4.34	0	Hydrophobic	false
CE3	CZ3	TRP- 693	3.48	0	Hydrophobic	false
CG	CH2	TRP- 693	3.76	0	Hydrophobic	false
C6	CG2	VAL- 710	3.64	0	Hydrophobic	false
O2P	NE2	HIS- 711	2.95	163.96	H-Bond (Protein Donor)	false
O	NH1	ARG- 717	2.98	138.18	H-Bond (Protein Donor)	false
O	NH2	ARG- 717	2.88	143.02	H-Bond (Protein Donor)	false
O2P	ZN	ZN- 1750	1.96	0	Metal Acceptor	false