scPDB - 2xye entry

Protein Data Bank Entry:

PDB ID : 2xye

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2010-11-17

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	48 %
B	52 %

Ligand binding site composition:

B-Factor:	11.188
Number of residues:	44
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.936	880.875

% Hydrophobic	% Polar
41.00	59.00
According to VolSite

Ligand :

HET Code:	CXG
Formula:	C40H55N5O6
Molecular weight:	701.895 g/mol
DrugBank ID:	-
Buried Surface Area:	60.67 %
Polar Surface area:	149.09 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	5
Rings:	3
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	18

Mass center Coordinates

X	Y	Z
13.3574	21.7635	6.44939

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
CBB	CD2	LEU- 23	4.19	0	Hydrophobic	false
CG1	CB	ALA- 28	3.44	0	Hydrophobic	false
O	N	ASP- 29	2.82	170.56	H-Bond (Protein Donor)	false
CG1	CB	ASP- 30	4.46	0	Hydrophobic	false
CG2	CG1	VAL- 32	4.5	0	Hydrophobic	false
CAE	CB	ILE- 47	3.51	0	Hydrophobic	false
CG2	CD1	ILE- 47	4.28	0	Hydrophobic	false
NBG	O	GLY- 48	2.98	174.75	H-Bond (Ligand Donor)	false
CAH	CG1	ILE- 50	3.66	0	Hydrophobic	false
CAW	CG	PRO- 81	3.87	0	Hydrophobic	false
CAS	CB	PRO- 81	3.66	0	Hydrophobic	false
CAY	CG	PRO- 81	3.89	0	Hydrophobic	false
C53	CB	PRO- 81	3.79	0	Hydrophobic	false
CBP	CG2	THR- 82	3.45	0	Hydrophobic	false
CAX	CG2	THR- 82	3.44	0	Hydrophobic	false
CBB	CG2	VAL- 84	4.21	0	Hydrophobic	false
CAU	CD2	LEU- 123	3.35	0	Hydrophobic	false
OAM	OD2	ASP- 125	2.83	173.6	H-Bond (Ligand Donor)	false
NBH	O	GLY- 127	3.01	145.64	H-Bond (Ligand Donor)	false
CAG	CB	ALA- 128	4	0	Hydrophobic	false
OAJ	N	ASP- 129	2.82	160.47	H-Bond (Protein Donor)	false
CAF	CB	ASP- 130	4.38	0	Hydrophobic	false
CAG	CG1	VAL- 132	4.4	0	Hydrophobic	false
CAF	CD1	ILE- 147	4.28	0	Hydrophobic	false
CAH	CD1	ILE- 147	3.81	0	Hydrophobic	false
NBF	O	GLY- 148	3	174.17	H-Bond (Ligand Donor)	false
CG2	CG1	ILE- 150	3.4	0	Hydrophobic	false
C24	CG1	ILE- 150	4.18	0	Hydrophobic	false
CAW	CD1	ILE- 150	3.79	0	Hydrophobic	false
CAR	CZ	PHE- 153	2.97	0	Hydrophobic	false
CAP	CG	PRO- 181	3.52	0	Hydrophobic	false
CAN	CG2	THR- 182	3.49	0	Hydrophobic	false
CBA	CG1	VAL- 184	4.44	0	Hydrophobic	false
CAG	CG2	VAL- 184	4.09	0	Hydrophobic	false