scPDB - 3vyd entry

Protein Data Bank Entry:

PDB ID : 3vyd

Resolution :2.810 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:	43.599
Number of residues:	36
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.321	1073.250

% Hydrophobic	% Polar
43.08	56.92
According to VolSite

Ligand :

HET Code:	VYD
Formula:	C24H39ClN4O2
Molecular weight:	451.045 g/mol
DrugBank ID:	-
Buried Surface Area:	55.52 %
Polar Surface area:	70.46 Å2

Number of
H-Bond Acceptors:	2
H-Bond Donors:	3
Rings:	3
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	2
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
177.473	199.927	98.0684

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
C1	CG	GLN- 19	4.01	0	Hydrophobic	false
N25	OD2	ASP- 38	3	164.43	H-Bond (Ligand Donor)	false
N25	OD1	ASP- 38	2.72	128.64	H-Bond (Ligand Donor)	false
N25	OD2	ASP- 38	3	0	Ionic (Ligand Cationic)	false
N25	OD1	ASP- 38	2.72	0	Ionic (Ligand Cationic)	false
N28	O	GLY- 40	2.97	146.23	H-Bond (Ligand Donor)	false
C14	CB	SER- 41	4.43	0	Hydrophobic	false
C20	CB	SER- 41	3.68	0	Hydrophobic	false
C18	CD1	TYR- 83	3.83	0	Hydrophobic	false
C10	CD2	TYR- 83	3.7	0	Hydrophobic	false
C22	CD2	TYR- 83	3.78	0	Hydrophobic	false
O30	N	SER- 84	2.76	159.88	H-Bond (Protein Donor)	false
CL	CG	PRO- 118	3.58	0	Hydrophobic	false
C18	CE1	PHE- 119	4.33	0	Hydrophobic	false
CL	CE1	PHE- 119	3.41	0	Hydrophobic	false
C4	CB	ALA- 122	4.15	0	Hydrophobic	false
CL	CB	ALA- 122	4.45	0	Hydrophobic	false
CL	CZ	PHE- 124	3.84	0	Hydrophobic	false
C17	CG2	VAL- 127	4.13	0	Hydrophobic	false
C18	CG2	VAL- 127	4.08	0	Hydrophobic	false
C19	CD1	ILE- 137	3.73	0	Hydrophobic	false
N25	OD1	ASP- 226	3.05	142.55	H-Bond (Ligand Donor)	false
N25	OD2	ASP- 226	2.77	146.35	H-Bond (Ligand Donor)	false
N25	OD1	ASP- 226	3.05	0	Ionic (Ligand Cationic)	false
N25	OD2	ASP- 226	2.77	0	Ionic (Ligand Cationic)	false