scPDB - 1ajv entry

Protein Data Bank Entry:

PDB ID : 1ajv

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 1997-05-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Gag-Pol polyprotein
ID:	POL_HV1B1
AC:	P03366
Organism:	Human immunodeficiency virus type 1 group M subtype B
Reign:	Viruses
TaxID:	11678
EC Number:	3.4.23.16

Chains:

Chain Name:	Percentage of Residues within binding site
A	49 %
B	51 %

Ligand binding site composition:

B-Factor:	12.304
Number of residues:	46
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.702	732.375

% Hydrophobic	% Polar
43.78	56.22
According to VolSite

Ligand :

HET Code:	NMB
Formula:	C32H34N2O6S
Molecular weight:	574.687 g/mol
DrugBank ID:	-
Buried Surface Area:	71.96 %
Polar Surface area:	107.92 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	2
Rings:	5
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
12.5671	22.6949	5.30954

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
C29	CD2	LEU- 23	3.77	0	Hydrophobic	false
C36	CD2	LEU- 23	3.58	0	Hydrophobic	false
O30	OD2	ASP- 25	3.21	129.32	H-Bond (Ligand Donor)	false
O30	OD1	ASP- 25	2.78	166.4	H-Bond (Ligand Donor)	false
O31	OD2	ASP- 25	2.66	177.95	H-Bond (Ligand Donor)	false
O31	OD1	ASP- 25	3.12	121.85	H-Bond (Ligand Donor)	false
O30	OD1	ASP- 25	3.46	127.2	H-Bond (Protein Donor)	false
O31	OD1	ASP- 25	2.67	149.69	H-Bond (Protein Donor)	false
C05	CB	ALA- 28	4.48	0	Hydrophobic	false
C41	CB	ALA- 28	3.97	0	Hydrophobic	false
C13	CB	ALA- 28	3.69	0	Hydrophobic	false
C17	CB	ALA- 28	3.54	0	Hydrophobic	false
C20	CB	ASP- 29	4.25	0	Hydrophobic	false
C12	CB	ASP- 30	4.11	0	Hydrophobic	false
C21	CB	ASP- 30	3.66	0	Hydrophobic	false
C13	CG1	VAL- 32	3.82	0	Hydrophobic	false
C22	CG2	VAL- 32	3.66	0	Hydrophobic	false
C11	CB	ILE- 47	4.37	0	Hydrophobic	false
C12	CD1	ILE- 47	4.13	0	Hydrophobic	false
C19	CB	ILE- 47	4.39	0	Hydrophobic	false
C20	CG2	ILE- 47	3.95	0	Hydrophobic	false
C21	CD1	ILE- 47	3.95	0	Hydrophobic	false
C04	CD1	ILE- 50	4.04	0	Hydrophobic	false
C32	CD1	ILE- 50	3.67	0	Hydrophobic	false
C14	CD1	ILE- 50	3.51	0	Hydrophobic	false
O15	N	ILE- 50	2.86	162.73	H-Bond (Protein Donor)	false
O40	N	ILE- 50	2.87	136.42	H-Bond (Protein Donor)	false
C26	CG	PRO- 81	3.91	0	Hydrophobic	false
C39	CB	PRO- 81	3.5	0	Hydrophobic	false
C26	CG1	VAL- 82	3.39	0	Hydrophobic	false
C37	CG2	VAL- 82	3.86	0	Hydrophobic	false
C05	CD1	ILE- 84	4.49	0	Hydrophobic	false
C13	CG2	ILE- 84	4.24	0	Hydrophobic	false
C14	CD1	ILE- 84	4.19	0	Hydrophobic	false
C32	CD1	ILE- 84	3.81	0	Hydrophobic	false
C23	CD1	ILE- 84	3.75	0	Hydrophobic	false