scPDB - 1dif entry

Protein Data Bank Entry:

PDB ID : 1dif

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 1995-10-09

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_HV1BR
AC:	P03367
Organism:	Human immunodeficiency virus type 1 group M subtype B
Reign:	Viruses
TaxID:	11686
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	17.613
Number of residues:	45
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.267	1012.500

% Hydrophobic	% Polar
45.00	55.00
According to VolSite

Ligand :

HET Code:	A85
Formula:	C44H56F2N8O6
Molecular weight:	830.962 g/mol
DrugBank ID:	-
Buried Surface Area:	63.33 %
Polar Surface area:	189.11 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	6
Rings:	4
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	19

Mass center Coordinates

X	Y	Z
5.09017	-1.54037	14.5132

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
DuAr	CZ	ARG- 8	3.61	14.42	Pi/Cation	false
DuAr	CZ	ARG- 8	3.64	11.91	Pi/Cation	false
C9	CD	ARG- 8	3.49	0	Hydrophobic	false
C13	CD	ARG- 8	3.73	0	Hydrophobic	false
C9	CD2	LEU- 23	3.96	0	Hydrophobic	false
C39	CD2	LEU- 23	4.4	0	Hydrophobic	false
C58	CD2	LEU- 23	4.42	0	Hydrophobic	false
C13	CD2	LEU- 23	3.79	0	Hydrophobic	false
O47	OD2	ASP- 25	2.65	158.69	H-Bond (Ligand Donor)	false
O48	OD1	ASP- 25	2.83	154.27	H-Bond (Ligand Donor)	false
O48	OD2	ASP- 25	3.14	134.29	H-Bond (Ligand Donor)	false
C26	CB	ALA- 28	4.13	0	Hydrophobic	false
F1	CB	ALA- 28	4.35	0	Hydrophobic	false
F2	CB	ALA- 28	3.89	0	Hydrophobic	false
C87	CB	ALA- 28	4.46	0	Hydrophobic	false
O2	N	ASP- 29	3.03	165.2	H-Bond (Protein Donor)	false
O98	N	ASP- 29	2.89	163.42	H-Bond (Protein Donor)	false
C27	CB	ASP- 30	4.45	0	Hydrophobic	false
C26	CG2	VAL- 32	4.17	0	Hydrophobic	false
C27	CG2	VAL- 32	3.97	0	Hydrophobic	false
C86	CG2	VAL- 32	4.21	0	Hydrophobic	false
C87	CG2	VAL- 32	4.05	0	Hydrophobic	false
C27	CD1	ILE- 47	4.45	0	Hydrophobic	false
C86	CD1	ILE- 47	4.04	0	Hydrophobic	false
N21	O	GLY- 48	3	167.69	H-Bond (Ligand Donor)	false
N81	O	GLY- 48	3.03	158.44	H-Bond (Ligand Donor)	false
C26	CG1	ILE- 50	3.66	0	Hydrophobic	false
C44	CG1	ILE- 50	3.93	0	Hydrophobic	false
C54	CG1	ILE- 50	4.02	0	Hydrophobic	false
C87	CG1	ILE- 50	3.92	0	Hydrophobic	false
C43	CG	PRO- 81	3.83	0	Hydrophobic	false
C56	CG	PRO- 81	3.85	0	Hydrophobic	false
C11	CG2	VAL- 82	3.88	0	Hydrophobic	false
C15	CG2	VAL- 82	4.17	0	Hydrophobic	false
C42	CG2	VAL- 82	3.99	0	Hydrophobic	false
C57	CG1	VAL- 82	3.69	0	Hydrophobic	false
C26	CD1	ILE- 84	3.7	0	Hydrophobic	false
C87	CD1	ILE- 84	3.59	0	Hydrophobic	false
C45	CD1	ILE- 84	3.78	0	Hydrophobic	false
C54	CD1	ILE- 84	3.66	0	Hydrophobic	false