scPDB - 3kdc entry

Protein Data Bank Entry:

PDB ID : 3kdc

Resolution :2.200 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	47 %
B	53 %

Ligand binding site composition:

B-Factor:	21.493
Number of residues:	46
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.977	870.750

% Hydrophobic	% Polar
43.41	56.59
According to VolSite

Ligand :

HET Code:	JZP
Formula:	C33H35Cl2N3O6S
Molecular weight:	672.618 g/mol
DrugBank ID:	-
Buried Surface Area:	71.01 %
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
16.1281	22.5461	17.2686

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	4.23	0	Hydrophobic	false
C30	CD2	LEU- 23	3.35	0	Hydrophobic	false
O3	OD2	ASP- 25	2.91	140.32	H-Bond (Protein Donor)	false
O5	OD2	ASP- 25	3	128.81	H-Bond (Protein Donor)	false
O5	OD1	ASP- 25	2.53	156.21	H-Bond (Ligand Donor)	false
O5	OD2	ASP- 25	3.09	128.38	H-Bond (Ligand Donor)	false
N4	O	GLY- 27	3.44	149.62	H-Bond (Ligand Donor)	false
CL1	CB	ALA- 28	4.08	0	Hydrophobic	false
C34	CB	ALA- 28	3.62	0	Hydrophobic	false
O7	N	ASP- 29	3.45	169.72	H-Bond (Protein Donor)	false
C39	CB	ASP- 29	4.17	0	Hydrophobic	false
C40	CB	ASP- 29	3.65	0	Hydrophobic	false
C41	CB	ASP- 30	4.05	0	Hydrophobic	false
C37	CB	ASP- 30	3.82	0	Hydrophobic	false
CL1	CB	ASP- 30	3.81	0	Hydrophobic	false
CL1	CG2	VAL- 32	3.75	0	Hydrophobic	false
C38	CG1	VAL- 32	3.48	0	Hydrophobic	false
CL1	CD1	ILE- 47	4.01	0	Hydrophobic	false
C42	CB	ILE- 47	4.09	0	Hydrophobic	false
C39	CB	ILE- 47	4.26	0	Hydrophobic	false
C41	CG2	ILE- 47	3.54	0	Hydrophobic	false
C38	CD1	ILE- 47	3.99	0	Hydrophobic	false
C37	CD1	ILE- 47	3.96	0	Hydrophobic	false
C21	CD1	ILE- 50	4.3	0	Hydrophobic	false
S1	CG1	ILE- 50	4.16	0	Hydrophobic	false
C23	CD1	ILE- 50	4.06	0	Hydrophobic	false
C34	CD1	ILE- 50	3.75	0	Hydrophobic	false
C37	CD1	LEU- 76	4.44	0	Hydrophobic	false
C24	CG	PRO- 81	3.48	0	Hydrophobic	false
C26	CG2	VAL- 82	3.48	0	Hydrophobic	false
C30	CG1	VAL- 82	3.32	0	Hydrophobic	false
C30	CG2	ILE- 84	3.85	0	Hydrophobic	false
C34	CD1	ILE- 84	3.87	0	Hydrophobic	false
C38	CG2	ILE- 84	4.42	0	Hydrophobic	false
C22	CD1	ILE- 84	4.2	0	Hydrophobic	false