scPDB - 2zd1 entry

Protein Data Bank Entry:

PDB ID : 2zd1

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2007-11-16

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:	2.7.7.49

Chains:

Chain Name:	Percentage of Residues within binding site
A	93 %
B	7 %

Ligand binding site composition:

B-Factor:	33.164
Number of residues:	30
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.520	577.125

% Hydrophobic	% Polar
67.25	32.75
According to VolSite

Ligand :

HET Code:	T27
Formula:	C22H18N6
Molecular weight:	366.419 g/mol
DrugBank ID:	DB08864
Buried Surface Area:	77.86 %
Polar Surface area:	97.42 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	2
Rings:	3
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
50.4819	-27.5147	37.0398

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
C7	CG	PRO- 95	3.94	0	Hydrophobic	false
C7	CD2	LEU- 100	3.87	0	Hydrophobic	false
C10	CD2	LEU- 100	4.05	0	Hydrophobic	false
C17	CD1	LEU- 100	4.15	0	Hydrophobic	false
N2	N	LYS- 101	3.21	176.24	H-Bond (Protein Donor)	false
N4	O	LYS- 101	2.7	147.03	H-Bond (Ligand Donor)	false
C14	CB	LYS- 103	4.25	0	Hydrophobic	false
C15	CG	LYS- 103	3.63	0	Hydrophobic	false
C13	CG2	VAL- 106	3.98	0	Hydrophobic	false
C10	CG	GLU- 138	4.13	0	Hydrophobic	false
C8	CG2	VAL- 179	3.79	0	Hydrophobic	false
C10	CB	VAL- 179	4.05	0	Hydrophobic	false
C7	CD1	TYR- 181	3.94	0	Hydrophobic	false
C2	CD2	TYR- 181	3.43	0	Hydrophobic	false
C5	CB	TYR- 181	3.78	0	Hydrophobic	false
C6	CB	TYR- 181	3.57	0	Hydrophobic	false
C4	CB	TYR- 188	3.56	0	Hydrophobic	false
C7	CH2	TRP- 229	4.43	0	Hydrophobic	false
C13	CB	LEU- 234	4.35	0	Hydrophobic	false
C18	CD1	LEU- 234	4.16	0	Hydrophobic	false
C2	CD1	LEU- 234	4.05	0	Hydrophobic	false