scPDB - 2wkz entry

Protein Data Bank Entry:

PDB ID : 2wkz

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2009-06-19

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	47 %
B	53 %

Ligand binding site composition:

B-Factor:	10.640
Number of residues:	43
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.916	864.000

% Hydrophobic	% Polar
42.19	57.81
According to VolSite

Ligand :

HET Code:	5AH
Formula:	C40H47N5O6
Molecular weight:	693.831 g/mol
DrugBank ID:	-
Buried Surface Area:	66.94 %
Polar Surface area:	153.12 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	5
Rings:	5
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	15

Mass center Coordinates

X	Y	Z
13.4	22.1118	6.49849

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
C33	CD2	LEU- 23	4.46	0	Hydrophobic	false
C39	CD2	LEU- 23	4.25	0	Hydrophobic	false
N20	O	GLY- 27	3.27	172.86	H-Bond (Ligand Donor)	false
C29	CB	ALA- 28	3.64	0	Hydrophobic	false
O23	N	ASP- 29	2.98	161.34	H-Bond (Protein Donor)	false
C24	CB	ASP- 29	4.27	0	Hydrophobic	false
C26	CB	ASP- 30	4.08	0	Hydrophobic	false
C27	CG1	VAL- 32	3.49	0	Hydrophobic	false
C27	CD1	ILE- 47	3.91	0	Hydrophobic	false
C48	CG1	ILE- 50	3.62	0	Hydrophobic	false
C36	CG	PRO- 81	3.87	0	Hydrophobic	false
C37	CB	PRO- 81	3.98	0	Hydrophobic	false
C5	CB	PRO- 81	3.54	0	Hydrophobic	false
C39	CG1	VAL- 82	3.74	0	Hydrophobic	false
C28	CD1	ILE- 84	3.8	0	Hydrophobic	false
C33	CD1	ILE- 84	3.62	0	Hydrophobic	false
C14	CD2	LEU- 123	3.5	0	Hydrophobic	false
O11	OD2	ASP- 125	2.72	168.92	H-Bond (Ligand Donor)	false
N40	O	GLY- 127	3.21	162.41	H-Bond (Ligand Donor)	false
C48	CB	ALA- 128	3.79	0	Hydrophobic	false
C45	CB	ASP- 129	4.38	0	Hydrophobic	false
O46	N	ASP- 129	2.88	157.3	H-Bond (Protein Donor)	false
C49	CB	ASP- 130	4.34	0	Hydrophobic	false
C48	CG1	VAL- 132	4.34	0	Hydrophobic	false
C1	CD1	ILE- 147	3.88	0	Hydrophobic	false
C49	CD1	ILE- 147	4.38	0	Hydrophobic	false
N51	O	GLY- 148	3.01	167.78	H-Bond (Ligand Donor)	false
C35	CG2	ILE- 150	3.94	0	Hydrophobic	false
C30	CD1	ILE- 150	3.68	0	Hydrophobic	false
C29	CD1	ILE- 150	3.74	0	Hydrophobic	false
C17	CB	PRO- 181	3.83	0	Hydrophobic	false
C16	CG1	VAL- 182	3.94	0	Hydrophobic	false
C14	CG2	VAL- 182	3.8	0	Hydrophobic	false
C48	CD1	ILE- 184	3.74	0	Hydrophobic	false
C12	CD1	ILE- 184	3.45	0	Hydrophobic	false