scPDB - 4njv entry

Protein Data Bank Entry:

PDB ID : 4njv

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2013-11-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Protease
ID:	Q9J006_9HIV1
AC:	Q9J006
Organism:	Human immunodeficiency virus 1
Reign:	Viruses
TaxID:	11676
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	47 %
B	53 %

Ligand binding site composition:

B-Factor:	18.299
Number of residues:	43
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.960	941.625

% Hydrophobic	% Polar
37.63	62.37
According to VolSite

Ligand :

HET Code:	RIT
Formula:	C37H48N6O5S2
Molecular weight:	720.944 g/mol
DrugBank ID:	DB00503
Buried Surface Area:	60.51 %
Polar Surface area:	202.26 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	4
Rings:	4
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	18

Mass center Coordinates

X	Y	Z
18.4641	4.99336	2.3779

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
S81	CD	ARG- 8	4.04	0	Hydrophobic	false
DuAr	CZ	ARG- 8	3.38	15.01	Pi/Cation	false
C31	CD2	LEU- 23	4.26	0	Hydrophobic	false
C44	CD2	LEU- 23	4.12	0	Hydrophobic	false
O41	OD2	ASP- 25	2.69	167.2	H-Bond (Ligand Donor)	false
O41	OD1	ASP- 25	2.74	121.84	H-Bond (Ligand Donor)	false
O41	OD1	ASP- 25	2.67	146.88	H-Bond (Protein Donor)	false
N11	O	GLY- 27	3.21	127.37	H-Bond (Ligand Donor)	false
N58	O	GLY- 27	2.96	151	H-Bond (Ligand Donor)	false
C68	CB	ALA- 28	4.02	0	Hydrophobic	false
O76	N	ASP- 29	2.95	163.35	H-Bond (Protein Donor)	false
N5	N	ASP- 30	3.17	132.55	H-Bond (Protein Donor)	false
C64	CG2	VAL- 32	3.71	0	Hydrophobic	false
S3	CB	ILE- 47	4.13	0	Hydrophobic	false
C64	CD1	ILE- 47	4.41	0	Hydrophobic	false
N20	O	GLY- 48	3.18	158.48	H-Bond (Ligand Donor)	false
C6	CG1	ILE- 50	4.05	0	Hydrophobic	false
C52	CG1	ILE- 50	4.21	0	Hydrophobic	false
C35	CD1	ILE- 50	3.9	0	Hydrophobic	false
C68	CD1	ILE- 50	3.66	0	Hydrophobic	false
C50	CG	PRO- 81	3.25	0	Hydrophobic	false
C86	CB	PRO- 81	3.5	0	Hydrophobic	false
S81	CG2	THR- 82	3.91	0	Hydrophobic	false
C86	CB	THR- 82	3.57	0	Hydrophobic	false
C45	CG2	THR- 82	3.91	0	Hydrophobic	false
C14	CD1	ILE- 84	4.48	0	Hydrophobic	false
C68	CD1	ILE- 84	3.86	0	Hydrophobic	false
C28	CD1	ILE- 84	3.77	0	Hydrophobic	false
C35	CD1	ILE- 84	3.47	0	Hydrophobic	false
C44	CD1	ILE- 84	3.57	0	Hydrophobic	false