scPDB - 1izi entry

Protein Data Bank Entry:

PDB ID : 1izi

Resolution :2.150 Å

Experimental Method : X-ray

Deposition Date : 2002-10-02

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	48 %
B	52 %

Ligand binding site composition:

B-Factor:	36.383
Number of residues:	42
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.682	712.125

% Hydrophobic	% Polar
41.23	58.77
According to VolSite

Ligand :

HET Code:	Q50
Formula:	C38H47N5O7
Molecular weight:	685.809 g/mol
DrugBank ID:	DB04353
Buried Surface Area:	62.22 %
Polar Surface area:	199.77 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:	2
Rotatable Bonds:	20

Mass center Coordinates

X	Y	Z
-7.29756	15.6769	-1.75822

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
C27	CD2	LEU- 23	3.71	0	Hydrophobic	false
C12	CD2	LEU- 23	3.71	0	Hydrophobic	false
O18	OD1	ASP- 25	2.76	148.03	H-Bond (Ligand Donor)	false
O18	OD2	ASP- 25	2.73	141.31	H-Bond (Ligand Donor)	false
N30	O	GLY- 27	2.93	161.13	H-Bond (Ligand Donor)	false
N8	O	GLY- 27	2.86	156.31	H-Bond (Ligand Donor)	false
C32	CB	ALA- 28	3.76	0	Hydrophobic	false
C2	CB	ALA- 28	3.78	0	Hydrophobic	false
O38	N	ASP- 29	3	169.97	H-Bond (Protein Donor)	false
O35	N	ASP- 30	3.04	152.79	H-Bond (Protein Donor)	false
N36	OD1	ASP- 30	3.07	168.6	H-Bond (Ligand Donor)	false
C2	CB	ASP- 30	3.94	0	Hydrophobic	false
C33	CG2	VAL- 32	4.21	0	Hydrophobic	false
C4	CG2	VAL- 32	3.65	0	Hydrophobic	false
C2	CG2	VAL- 32	4.31	0	Hydrophobic	false
C33	CD1	ILE- 47	4.12	0	Hydrophobic	false
C3	CD1	ILE- 47	3.66	0	Hydrophobic	false
O49	N	GLY- 48	2.83	176.99	H-Bond (Protein Donor)	false
N39	O	GLY- 48	2.91	170.1	H-Bond (Ligand Donor)	false
C4	CD1	ILE- 50	3.58	0	Hydrophobic	false
C3	CG2	ILE- 50	4.46	0	Hydrophobic	false
C44	CG	PRO- 81	4.26	0	Hydrophobic	false
C45	CB	PRO- 81	4.43	0	Hydrophobic	false
C24	CB	PRO- 81	3.92	0	Hydrophobic	false
C15	CG	PRO- 81	3.46	0	Hydrophobic	false
C14	CB	THR- 82	3.89	0	Hydrophobic	false
C13	CG2	THR- 82	3.79	0	Hydrophobic	false
C24	CG2	THR- 82	3.57	0	Hydrophobic	false
C4	CG2	VAL- 84	4	0	Hydrophobic	false
C21	CG1	VAL- 84	4.03	0	Hydrophobic	false
C10	CG1	VAL- 84	4.03	0	Hydrophobic	false