scPDB - 3vyf entry

Protein Data Bank Entry:

PDB ID : 3vyf

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2012-09-24

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:	32.599
Number of residues:	41
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.407	1130.625

% Hydrophobic	% Polar
44.78	55.22
According to VolSite

Ligand :

HET Code:	VYF
Formula:	C27H44ClN4O2
Molecular weight:	492.117 g/mol
DrugBank ID:	-
Buried Surface Area:	58.02 %
Polar Surface area:	69.26 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	2
Rings:	3
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
178.609	200.729	99.237

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
C20	CG	GLN- 19	3.7	0	Hydrophobic	false
C15	CG2	VAL- 36	3.71	0	Hydrophobic	false
N3	OD2	ASP- 38	3.31	143.35	H-Bond (Ligand Donor)	false
N3	OD1	ASP- 38	2.86	152.48	H-Bond (Ligand Donor)	false
N3	OD2	ASP- 38	3.31	0	Ionic (Ligand Cationic)	false
N3	OD1	ASP- 38	2.86	0	Ionic (Ligand Cationic)	false
C15	CB	ASP- 38	3.75	0	Hydrophobic	false
N25	O	GLY- 40	3.11	172.5	H-Bond (Ligand Donor)	false
C34	CB	SER- 41	3.45	0	Hydrophobic	false
C14	CD1	TYR- 83	3.74	0	Hydrophobic	false
C27	CD2	TYR- 83	3.75	0	Hydrophobic	false
C6	CD2	TYR- 83	3.54	0	Hydrophobic	false
O24	N	SER- 84	2.84	160.16	H-Bond (Protein Donor)	false
O13	OG1	THR- 85	2.62	139.95	H-Bond (Protein Donor)	false
C18	CB	PRO- 118	4.43	0	Hydrophobic	false
CL1	CG	PRO- 118	3.66	0	Hydrophobic	false
CL1	CE1	PHE- 119	3.47	0	Hydrophobic	false
C18	CB	ALA- 122	4.16	0	Hydrophobic	false
CL1	CZ	PHE- 124	3.98	0	Hydrophobic	false
C14	CG2	VAL- 127	4.23	0	Hydrophobic	false
C15	CG1	VAL- 127	4.01	0	Hydrophobic	false
C33	CD1	ILE- 137	3.43	0	Hydrophobic	false
C30	CD2	LEU- 224	4.19	0	Hydrophobic	false
N3	OD2	ASP- 226	2.6	165.68	H-Bond (Ligand Donor)	false
N3	OD1	ASP- 226	2.86	123.36	H-Bond (Ligand Donor)	false
N3	OD2	ASP- 226	2.6	0	Ionic (Ligand Cationic)	false
N3	OD1	ASP- 226	2.86	0	Ionic (Ligand Cationic)	false
C31	CG2	ILE- 305	3.77	0	Hydrophobic	false
C30	CG2	THR- 309	3.95	0	Hydrophobic	false