scPDB - 1pro entry

Protein Data Bank Entry:

PDB ID : 1pro

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 1995-07-18

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_HV1Z2
AC:	P12499
Organism:	Human immunodeficiency virus type 1 group M subtype D
Reign:	Viruses
TaxID:	11683
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	50 %
B	50 %

Ligand binding site composition:

B-Factor:	21.753
Number of residues:	43
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.713	661.500

% Hydrophobic	% Polar
38.27	61.73
According to VolSite

Ligand :

HET Code:	A88
Formula:	C34H38N3O6
Molecular weight:	584.682 g/mol
DrugBank ID:	DB02804
Buried Surface Area:	73.88 %
Polar Surface area:	107.14 Å2

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

Mass center Coordinates

X	Y	Z
-9.39107	16.2417	27.8197

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
C10	CD1	LEU- 23	4.17	0	Hydrophobic	false
C17	CD1	LEU- 23	4.14	0	Hydrophobic	false
O6	OD2	ASP- 25	2.9	138	H-Bond (Ligand Donor)	false
O6	OD1	ASP- 25	2.95	158.29	H-Bond (Ligand Donor)	false
C27	CB	ALA- 28	3.59	0	Hydrophobic	false
C36	CB	ALA- 28	3.54	0	Hydrophobic	false
O30	N	ASP- 29	3.32	158.56	H-Bond (Protein Donor)	false
O40	N	ASP- 29	3.39	159.74	H-Bond (Protein Donor)	false
C31	CB	ASP- 29	4.25	0	Hydrophobic	false
C41	CB	ASP- 29	3.93	0	Hydrophobic	false
O29	O	ASP- 30	3.27	137.33	H-Bond (Ligand Donor)	false
O39	O	ASP- 30	3.16	129.48	H-Bond (Ligand Donor)	false
O29	N	ASP- 30	2.91	152.04	H-Bond (Protein Donor)	false
O39	N	ASP- 30	2.9	148.45	H-Bond (Protein Donor)	false
C27	CG1	VAL- 32	4.18	0	Hydrophobic	false
C35	CG1	VAL- 32	4.03	0	Hydrophobic	false
C35	CD1	ILE- 47	3.92	0	Hydrophobic	false
O3	N	ILE- 50	3.05	173.26	H-Bond (Protein Donor)	false
O3	N	ILE- 50	3.05	175.25	H-Bond (Protein Donor)	false
C14	CG1	ILE- 50	4.13	0	Hydrophobic	false
C21	CG1	ILE- 50	4.47	0	Hydrophobic	false
C28	CD1	ILE- 50	3.6	0	Hydrophobic	false
C34	CD1	ILE- 50	3.6	0	Hydrophobic	false
C13	CG	PRO- 81	3.37	0	Hydrophobic	false
C20	CG	PRO- 81	3.45	0	Hydrophobic	false
C19	CG2	VAL- 82	3.86	0	Hydrophobic	false
C12	CG2	VAL- 82	3.53	0	Hydrophobic	false
C34	CD1	ILE- 84	4.23	0	Hydrophobic	false
C35	CG2	ILE- 84	4.44	0	Hydrophobic	false
C8	CD1	ILE- 84	3.7	0	Hydrophobic	false
C21	CD1	ILE- 84	3.92	0	Hydrophobic	false
C28	CD1	ILE- 84	4.13	0	Hydrophobic	false