scPDB - 1a9m entry

Protein Data Bank Entry:

PDB ID : 1a9m

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 1998-04-08

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:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	44 %
B	56 %

Ligand binding site composition:

B-Factor:	27.872
Number of residues:	43
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.880	779.625

% Hydrophobic	% Polar
42.86	57.14
According to VolSite

Ligand :

HET Code:	U0E
Formula:	C28H53N8O6
Molecular weight:	597.770 g/mol
DrugBank ID:	-
Buried Surface Area:	60.72 %
Polar Surface area:	257.34 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	9
Rings:	1
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	20

Mass center Coordinates

X	Y	Z
40.3985	18.1926	65.0449

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
C16	CD2	LEU- 23	4.33	0	Hydrophobic	false
C10	CD1	LEU- 23	3.68	0	Hydrophobic	false
O2	OD2	ASP- 25	2.91	163.14	H-Bond (Ligand Donor)	false
N2	O	GLY- 27	3.24	157.1	H-Bond (Ligand Donor)	false
C1	CB	ALA- 28	4.08	0	Hydrophobic	false
C20	CB	ALA- 28	3.56	0	Hydrophobic	false
N5	OD2	ASP- 29	3.46	162.68	H-Bond (Ligand Donor)	false
O5	N	ASP- 29	3.11	155.92	H-Bond (Protein Donor)	false
O4	N	ASP- 30	3.28	142.65	H-Bond (Protein Donor)	false
N4	O	HIS- 48	3.04	142.86	H-Bond (Ligand Donor)	false
O6	N	HIS- 48	3.01	163.94	H-Bond (Protein Donor)	false
C1	CD1	ILE- 50	4.4	0	Hydrophobic	false
C15	CG1	ILE- 50	3.9	0	Hydrophobic	false
C19	CD1	ILE- 50	3.97	0	Hydrophobic	false
C7	CG	PRO- 81	3.9	0	Hydrophobic	false
C8	CB	PRO- 81	4.24	0	Hydrophobic	false
C16	CG2	VAL- 82	3.55	0	Hydrophobic	false
C27	CG2	VAL- 82	4.31	0	Hydrophobic	false
C9	CG2	VAL- 82	3.31	0	Hydrophobic	false
C5	CD1	ILE- 84	4.09	0	Hydrophobic	false
C14	CD1	ILE- 84	3.38	0	Hydrophobic	false