scPDB - 3vsw entry

Protein Data Bank Entry:

PDB ID : 3vsw

Resolution :3.000 Å

Experimental Method : X-ray

Deposition Date : 2012-05-11

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:	24.073
Number of residues:	48
Including
Standard Amino Acids:	48
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.393	1208.250

% Hydrophobic	% Polar
46.09	53.91
According to VolSite

Ligand :

HET Code:	R31
Formula:	C28H48N5O6
Molecular weight:	550.711 g/mol
DrugBank ID:	-
Buried Surface Area:	65.56 %
Polar Surface area:	162.06 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	4
Rings:	2
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	16

Mass center Coordinates

X	Y	Z
177.762	200.375	98.1396

Binding mode :

What is Poseview ?

2D View
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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
C9	CG	GLN- 19	4.29	0	Hydrophobic	false
C14	CG	GLN- 19	4	0	Hydrophobic	false
C18	CB	TYR- 20	3.8	0	Hydrophobic	false
N22	OD2	ASP- 38	3.72	0	Ionic (Ligand Cationic)	false
N22	OD1	ASP- 38	2.92	0	Ionic (Ligand Cationic)	false
N22	OD1	ASP- 38	2.92	171.35	H-Bond (Ligand Donor)	false
O24	OD2	ASP- 38	2.59	147.76	H-Bond (Ligand Donor)	false
O24	OD1	ASP- 38	2.99	121.4	H-Bond (Ligand Donor)	false
N27	O	GLY- 40	3.13	153.6	H-Bond (Ligand Donor)	false
C21	CD2	TYR- 83	3.95	0	Hydrophobic	false
O28	N	SER- 84	3.29	139.24	H-Bond (Protein Donor)	false
O39	OG1	THR- 85	2.68	135.95	H-Bond (Protein Donor)	false
C10	CB	PRO- 118	4.29	0	Hydrophobic	false
C11	CG	PRO- 118	3.71	0	Hydrophobic	false
C11	CB	ALA- 122	3.69	0	Hydrophobic	false
C14	CE1	PHE- 124	4.5	0	Hydrophobic	false
O36	NE2	GLN- 135	3.32	141.52	H-Bond (Protein Donor)	false
C35	CD1	ILE- 137	3.49	0	Hydrophobic	false
C18	CZ	TYR- 162	3.98	0	Hydrophobic	false
C37	CD1	LEU- 224	3.68	0	Hydrophobic	false
C38	CD2	LEU- 224	4.09	0	Hydrophobic	false
N22	OD2	ASP- 226	2.75	163.91	H-Bond (Ligand Donor)	false
N22	OD2	ASP- 226	2.75	0	Ionic (Ligand Cationic)	false
N22	OD1	ASP- 226	2.92	0	Ionic (Ligand Cationic)	false
C38	CB	ASP- 226	4.46	0	Hydrophobic	false
N22	O	GLY- 228	3	167.24	H-Bond (Ligand Donor)	false
C16	CB	SER- 230	4.4	0	Hydrophobic	false
C37	CG2	ILE- 305	3.76	0	Hydrophobic	false
C38	CD1	ILE- 305	3.64	0	Hydrophobic	false
C37	CG2	THR- 309	4.13	0	Hydrophobic	false