scPDB - 2v13 entry

Protein Data Bank Entry:

PDB ID : 2v13

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2007-05-21

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Renin
ID:	RENI_HUMAN
AC:	P00797
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.4.23.15

Chains:

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

Ligand binding site composition:

B-Factor:	15.000
Number of residues:	43
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.469	975.375

% Hydrophobic	% Polar
51.56	48.44
According to VolSite

Ligand :

HET Code:	C40
Formula:	C25H44N3O5
Molecular weight:	466.634 g/mol
DrugBank ID:	-
Buried Surface Area:	63.11 %
Polar Surface area:	124.53 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	4
Rings:	1
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	17

Mass center Coordinates

X	Y	Z
82.8466	18.3607	-37.624

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
C1	CB	TYR- 20	3.99	0	Hydrophobic	false
O2	N	TYR- 20	2.78	159.71	H-Bond (Protein Donor)	false
C1	CG1	VAL- 36	4.2	0	Hydrophobic	false
C3	CG1	VAL- 36	3.77	0	Hydrophobic	false
N21	OD2	ASP- 38	3.39	143.73	H-Bond (Ligand Donor)	false
N21	OD1	ASP- 38	3.04	159.01	H-Bond (Ligand Donor)	false
O23	OD2	ASP- 38	2.62	163.68	H-Bond (Ligand Donor)	false
N21	OD2	ASP- 38	3.39	0	Ionic (Ligand Cationic)	false
N21	OD1	ASP- 38	3.04	0	Ionic (Ligand Cationic)	false
N29	O	GLY- 40	3.17	127.71	H-Bond (Ligand Donor)	false
C31	CB	SER- 41	4.04	0	Hydrophobic	false
C33	CB	ARG- 82	4.02	0	Hydrophobic	false
C19	CD1	TYR- 83	3.6	0	Hydrophobic	false
C22	CD1	TYR- 83	3.77	0	Hydrophobic	false
C31	CD1	TYR- 83	3.76	0	Hydrophobic	false
C24	CB	SER- 84	4.25	0	Hydrophobic	false
O28	N	SER- 84	2.86	154.18	H-Bond (Protein Donor)	false
O14	OG1	THR- 85	2.56	172.01	H-Bond (Protein Donor)	false
C11	CG	PRO- 118	3.5	0	Hydrophobic	false
C10	CB	ALA- 122	3.84	0	Hydrophobic	false
C5	CE2	PHE- 124	3.7	0	Hydrophobic	false
C18	CG2	VAL- 127	3.78	0	Hydrophobic	false
C33	CD1	ILE- 137	3.49	0	Hydrophobic	false
C1	CZ	TYR- 162	4.37	0	Hydrophobic	false
C26	CD2	LEU- 224	4.14	0	Hydrophobic	false
N21	OD1	ASP- 226	3.38	150.99	H-Bond (Ligand Donor)	false
N21	OD1	ASP- 226	3.38	0	Ionic (Ligand Cationic)	false
N21	OD2	ASP- 226	3.07	0	Ionic (Ligand Cationic)	false
C26	CG2	ILE- 305	4.41	0	Hydrophobic	false
C26	CG2	THR- 309	4.29	0	Hydrophobic	false