scPDB - 1rne entry

Protein Data Bank Entry:

PDB ID : 1rne

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 1991-12-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	9.160	9.160	9.160	0.000	9.160	1

List of CHEMBLId :

CHEMBL293196

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:	29.546
Number of residues:	53
Including
Standard Amino Acids:	50
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.387	1289.250

% Hydrophobic	% Polar
48.17	51.83
According to VolSite

Ligand :

HET Code:	C60
Formula:	C39H63N5O6S
Molecular weight:	730.012 g/mol
DrugBank ID:	-
Buried Surface Area:	63.5 %
Polar Surface area:	178.72 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	21

Mass center Coordinates

X	Y	Z
10.5789	13.8062	66.186

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
C3F	CG	GLN- 13	3.97	0	Hydrophobic	false
C2C	CG1	VAL- 30	4.17	0	Hydrophobic	false
CBC	CB	ASP- 32	4.29	0	Hydrophobic	false
C2C	CB	ASP- 32	4.44	0	Hydrophobic	false
NT	O	GLY- 34	2.83	142.22	H-Bond (Ligand Donor)	false
C2T	CB	SER- 35	3.48	0	Hydrophobic	false
C4T	CB	LEU- 73	4.12	0	Hydrophobic	false
CBC	CD1	TYR- 75	4.24	0	Hydrophobic	false
C5C	CG	TYR- 75	4.28	0	Hydrophobic	false
C6C	CD1	TYR- 75	3.6	0	Hydrophobic	false
CC	CD1	TYR- 75	4.31	0	Hydrophobic	false
C2T	CD1	TYR- 75	3.82	0	Hydrophobic	false
C4T	CE1	TYR- 75	4.38	0	Hydrophobic	false
CBH	CB	SER- 76	3.58	0	Hydrophobic	false
CNV	CB	SER- 76	4.16	0	Hydrophobic	false
N1H	OG	SER- 76	3.2	157.35	H-Bond (Ligand Donor)	false
OV	N	SER- 76	3.35	131.46	H-Bond (Protein Donor)	false
CAF	CG2	THR- 77	4.3	0	Hydrophobic	false
CBH	CG2	THR- 77	4.03	0	Hydrophobic	false
NH	OG1	THR- 77	3.2	177.39	H-Bond (Ligand Donor)	false
OH	N	THR- 77	3.24	138.82	H-Bond (Protein Donor)	false
C5F	CB	PRO- 111	3.91	0	Hydrophobic	false
C4C	CE1	PHE- 112	4.23	0	Hydrophobic	false
CS4	CD1	LEU- 114	4.42	0	Hydrophobic	false
C4F	CB	LEU- 114	4.18	0	Hydrophobic	false
C4F	CB	ALA- 115	4.07	0	Hydrophobic	false
C3C	CZ	PHE- 117	3.8	0	Hydrophobic	false
C4C	CG2	VAL- 120	4.05	0	Hydrophobic	false
C4T	CD1	ILE- 130	4.28	0	Hydrophobic	false
C2V	CD1	LEU- 213	4.12	0	Hydrophobic	false
NC	O	GLY- 217	3.34	141.28	H-Bond (Ligand Donor)	false
CNF	CB	SER- 219	4.36	0	Hydrophobic	false
OF	N	SER- 219	3.01	163.32	H-Bond (Protein Donor)	false
CS2	CE2	TYR- 220	3.61	0	Hydrophobic	false
N2H	OG	SER- 222	3.21	120.33	H-Bond (Protein Donor)	false
CBH	CE	MET- 289	3.82	0	Hydrophobic	false
C1V	CG2	ILE- 291	3.99	0	Hydrophobic	false
C2V	CD1	ILE- 291	4.24	0	Hydrophobic	false