scPDB - 3o9l entry

Protein Data Bank Entry:

PDB ID : 3o9l

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2010-08-04

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
C	83 %
D	17 %

Ligand binding site composition:

B-Factor:	38.250
Number of residues:	42
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.263	833.625

% Hydrophobic	% Polar
56.28	43.72
According to VolSite

Ligand :

HET Code:	LPN
Formula:	C35H42Cl3N2O4
Molecular weight:	661.078 g/mol
DrugBank ID:	-
Buried Surface Area:	67.19 %
Polar Surface area:	64.61 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	1
Rings:	5
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	14

Mass center Coordinates

X	Y	Z
-7.57302	-15.4731	-9.94641

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
C39	CG	GLN- 19	4.42	0	Hydrophobic	false
C42	CB	GLN- 19	4.21	0	Hydrophobic	false
C44	CB	TYR- 20	3.81	0	Hydrophobic	false
C42	CG2	VAL- 36	4.27	0	Hydrophobic	false
C44	CG2	VAL- 36	3.91	0	Hydrophobic	false
C32	CG1	VAL- 36	3.86	0	Hydrophobic	false
N28	OD1	ASP- 38	3.4	147.18	H-Bond (Ligand Donor)	false
N28	OD2	ASP- 38	3.41	159.15	H-Bond (Ligand Donor)	false
N28	OD1	ASP- 38	3.4	0	Ionic (Ligand Cationic)	false
N28	OD2	ASP- 38	3.41	0	Ionic (Ligand Cationic)	false
C31	CB	ASP- 38	4.28	0	Hydrophobic	false
C18	CB	SER- 41	4.2	0	Hydrophobic	false
C22	CB	SER- 41	4.32	0	Hydrophobic	false
CL1	CB	TRP- 45	4.47	0	Hydrophobic	false
C8	CB	TRP- 45	4.06	0	Hydrophobic	false
C4	CG	PRO- 47	3.78	0	Hydrophobic	false
CL1	CG	PRO- 47	3.8	0	Hydrophobic	false
C14	CD1	LEU- 81	3.87	0	Hydrophobic	false
C8	CG1	VAL- 88	4.38	0	Hydrophobic	false
CL1	CG2	VAL- 111	3.48	0	Hydrophobic	false
C4	CE	MET- 114	3.87	0	Hydrophobic	false
C8	CE	MET- 114	3.73	0	Hydrophobic	false
C2	CE	MET- 114	3.4	0	Hydrophobic	false
CL36	CG	PRO- 118	3.98	0	Hydrophobic	false
CL9	CE1	PHE- 119	3.92	0	Hydrophobic	false
CL36	CD1	PHE- 119	3.66	0	Hydrophobic	false
C12	CE1	PHE- 119	3.89	0	Hydrophobic	false
C37	CB	ALA- 122	3.83	0	Hydrophobic	false
CL9	CE2	PHE- 124	3.74	0	Hydrophobic	false
C32	CZ	PHE- 124	3.89	0	Hydrophobic	false
C34	CZ	PHE- 124	3.39	0	Hydrophobic	false
CL9	CG1	VAL- 127	4.42	0	Hydrophobic	false
C12	CG1	VAL- 127	4.14	0	Hydrophobic	false
C16	CG1	VAL- 127	4.19	0	Hydrophobic	false
C31	CG2	VAL- 127	3.91	0	Hydrophobic	false
N28	OD1	ASP- 226	3.94	0	Ionic (Ligand Cationic)	false
N28	OD2	ASP- 226	3.39	0	Ionic (Ligand Cationic)	false
N28	OD2	ASP- 226	3.39	160.81	H-Bond (Ligand Donor)	false
C40	CB	SER- 230	4.21	0	Hydrophobic	false