scPDB - 1xl2 entry

Protein Data Bank Entry:

PDB ID : 1xl2

Resolution :1.500 Å

Experimental Method : X-ray

Deposition Date : 2004-09-30

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:	3.4.23.16

Chains:

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

Ligand binding site composition:

B-Factor:	15.429
Number of residues:	42
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.089	924.750

% Hydrophobic	% Polar
43.43	56.57
According to VolSite

Ligand :

HET Code:	189
Formula:	C33H44N3O4S
Molecular weight:	578.785 g/mol
DrugBank ID:	-
Buried Surface Area:	63.66 %
Polar Surface area:	91.91 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	1
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
20.1364	-2.72207	18.2965

Binding mode :

What is Poseview ?

2D View
3D View

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
C18	CD2	LEU- 23	4.23	0	Hydrophobic	false
N23	OD2	ASP- 25	2.61	165.74	H-Bond (Ligand Donor)	false
N23	OD1	ASP- 25	2.69	171.3	H-Bond (Ligand Donor)	false
N23	OD2	ASP- 25	2.98	121.28	H-Bond (Ligand Donor)	false
N23	OD2	ASP- 25	2.61	0	Ionic (Ligand Cationic)	false
N23	OD1	ASP- 25	2.71	0	Ionic (Ligand Cationic)	false
N23	OD1	ASP- 25	2.69	0	Ionic (Ligand Cationic)	false
N23	OD2	ASP- 25	2.98	0	Ionic (Ligand Cationic)	false
C32	CG1	VAL- 32	4.16	0	Hydrophobic	false
C1	CG2	VAL- 32	3.61	0	Hydrophobic	false
C31	CG2	VAL- 32	3.82	0	Hydrophobic	false
C33	CG1	ILE- 47	3.62	0	Hydrophobic	false
C32	CD1	ILE- 47	3.36	0	Hydrophobic	false
C1	CD1	ILE- 47	3.7	0	Hydrophobic	false
O14	N	ILE- 50	2.7	164.61	H-Bond (Protein Donor)	false
C36	CD1	ILE- 50	3.85	0	Hydrophobic	false
C3	CB	ILE- 50	3.78	0	Hydrophobic	false
C33	CG1	ILE- 50	3.83	0	Hydrophobic	false
C40	CG1	ILE- 50	3.93	0	Hydrophobic	false
C39	CG1	ILE- 50	3.88	0	Hydrophobic	false
C34	CD1	ILE- 50	3.3	0	Hydrophobic	false
C5	CG2	ILE- 50	3.51	0	Hydrophobic	false
C33	CG1	ILE- 54	3.81	0	Hydrophobic	false
C32	CD1	ILE- 54	3.7	0	Hydrophobic	false
C44	CB	THR- 80	4.35	0	Hydrophobic	false
C2	CB	THR- 80	4.39	0	Hydrophobic	false
C19	CG	PRO- 81	4.45	0	Hydrophobic	false
C18	CB	PRO- 81	4.38	0	Hydrophobic	false
C40	CG	PRO- 81	3.93	0	Hydrophobic	false
C18	CG1	VAL- 82	3.52	0	Hydrophobic	false
C20	CD1	ILE- 84	4.24	0	Hydrophobic	false
C19	CG2	ILE- 84	4.13	0	Hydrophobic	false
C2	CD1	ILE- 84	3.55	0	Hydrophobic	false
C3	CD1	ILE- 84	3.62	0	Hydrophobic	false
C30	CD1	ILE- 84	3.5	0	Hydrophobic	false