scPDB - 2bkt entry

Protein Data Bank Entry:

PDB ID : 2bkt

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2005-02-18

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
B	100 %

Ligand binding site composition:

B-Factor:	48.073
Number of residues:	42
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.428	1326.375

% Hydrophobic	% Polar
53.69	46.31
According to VolSite

Ligand :

HET Code:	RPF
Formula:	C31H38N3O5
Molecular weight:	532.651 g/mol
DrugBank ID:	-
Buried Surface Area:	68.39 %
Polar Surface area:	85.87 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	2
Rings:	5
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
124.309	17.707	44.1041

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
C35	CG	GLN- 14	3.68	0	Hydrophobic	false
N2	OD2	ASP- 33	3.15	137.95	H-Bond (Ligand Donor)	false
N2	OD2	ASP- 33	3.15	0	Ionic (Ligand Cationic)	false
N2	OD1	ASP- 33	3.5	0	Ionic (Ligand Cationic)	false
C24	CB	ASP- 33	4	0	Hydrophobic	false
C27	CB	SER- 36	3.83	0	Hydrophobic	false
C4	CB	TRP- 40	3.93	0	Hydrophobic	false
C31	CE3	TRP- 40	3.31	0	Hydrophobic	false
C32	CD2	TRP- 40	3.71	0	Hydrophobic	false
C33	CB	TRP- 40	4.4	0	Hydrophobic	false
C8	CG	PRO- 42	3.33	0	Hydrophobic	false
C7	CB	HIS- 56	4.37	0	Hydrophobic	false
C32	CG2	VAL- 83	3.77	0	Hydrophobic	false
C4	CG2	VAL- 106	4.08	0	Hydrophobic	false
C32	CG2	VAL- 106	3.95	0	Hydrophobic	false
C33	SD	MET- 109	4.29	0	Hydrophobic	false
C8	SD	MET- 109	3.33	0	Hydrophobic	false
C36	CG	PRO- 113	3.74	0	Hydrophobic	false
C2	CD2	PHE- 114	3.44	0	Hydrophobic	false
C5	CB	PHE- 114	3.71	0	Hydrophobic	false
C33	CE2	PHE- 114	3.5	0	Hydrophobic	false
C34	CB	LEU- 116	4.18	0	Hydrophobic	false
C5	CB	ALA- 117	3.61	0	Hydrophobic	false
C34	CB	ALA- 117	3.55	0	Hydrophobic	false
C1	CD2	PHE- 119	3.8	0	Hydrophobic	false
C35	CE1	PHE- 119	4.14	0	Hydrophobic	false
C11	CZ	PHE- 119	3.41	0	Hydrophobic	false
C34	CZ	PHE- 119	3.9	0	Hydrophobic	false
C1	CB	VAL- 122	4.42	0	Hydrophobic	false
C14	CG2	VAL- 122	4.49	0	Hydrophobic	false
C24	CG2	VAL- 122	4.37	0	Hydrophobic	false
C28	CG2	VAL- 122	3.53	0	Hydrophobic	false
N2	OD2	ASP- 219	2.96	143.56	H-Bond (Ligand Donor)	false
N2	OD2	ASP- 219	2.96	0	Ionic (Ligand Cationic)	false
N1	O	HOH- 2003	3.11	152.04	H-Bond (Ligand Donor)	false