scPDB - 3kdb entry

Protein Data Bank Entry:

PDB ID : 3kdb

Resolution :1.660 Å

Experimental Method : X-ray

Deposition Date : 2009-10-22

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:	22.362
Number of residues:	46
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.189	465.750

% Hydrophobic	% Polar
42.03	57.97
According to VolSite

Ligand :

HET Code:	006
Formula:	C35H41N3O6S
Molecular weight:	631.782 g/mol
DrugBank ID:	-
Buried Surface Area:	70.35 %
Polar Surface area:	153.5 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	4
Rings:	5
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
16.4597	22.3698	17.5605

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	4.36	0	Hydrophobic	false
C52	CD2	LEU- 23	3.23	0	Hydrophobic	false
O20	OD1	ASP- 25	2.59	145.21	H-Bond (Ligand Donor)	false
O20	OD2	ASP- 25	2.88	133.85	H-Bond (Ligand Donor)	false
N2	O	GLY- 27	3.38	151.53	H-Bond (Ligand Donor)	false
N30	O	GLY- 27	3.32	148.83	H-Bond (Ligand Donor)	false
C44	CB	ALA- 28	4.15	0	Hydrophobic	false
C45	CB	ALA- 28	4.48	0	Hydrophobic	false
C34	CB	ALA- 28	3.49	0	Hydrophobic	false
O30	N	ASP- 29	3.21	164.05	H-Bond (Protein Donor)	false
C39	CB	ASP- 29	4.46	0	Hydrophobic	false
C40	CB	ASP- 29	3.7	0	Hydrophobic	false
C37	CB	ASP- 30	4.14	0	Hydrophobic	false
C47	CB	ASP- 30	3.68	0	Hydrophobic	false
C44	CG2	VAL- 32	3.51	0	Hydrophobic	false
C38	CG1	VAL- 32	3.69	0	Hydrophobic	false
C44	CD1	ILE- 47	3.89	0	Hydrophobic	false
C39	CB	ILE- 47	4.06	0	Hydrophobic	false
C38	CD1	ILE- 47	3.78	0	Hydrophobic	false
C47	CG2	ILE- 47	3.36	0	Hydrophobic	false
C23	CB	ILE- 50	4.39	0	Hydrophobic	false
C49	CD1	ILE- 50	4.27	0	Hydrophobic	false
S50	CG1	ILE- 50	4.18	0	Hydrophobic	false
C34	CD1	ILE- 50	3.98	0	Hydrophobic	false
C37	CD1	LEU- 76	4.38	0	Hydrophobic	false
S50	CG	PRO- 81	3.97	0	Hydrophobic	false
C53	CG	PRO- 81	4.34	0	Hydrophobic	false
C24	CG	PRO- 81	3.63	0	Hydrophobic	false
C26	CG2	VAL- 82	3.72	0	Hydrophobic	false
C52	CG2	VAL- 82	3.33	0	Hydrophobic	false
C34	CG2	ILE- 84	4.07	0	Hydrophobic	false
C52	CD1	ILE- 84	4.07	0	Hydrophobic	false
C22	CD1	ILE- 84	3.91	0	Hydrophobic	false
S50	CD1	ILE- 84	3.49	0	Hydrophobic	false