scPDB - 3dk1 entry

Protein Data Bank Entry:

PDB ID : 3dk1

Resolution :1.070 Å

Experimental Method : X-ray

Deposition Date : 2008-06-24

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	53 %
B	47 %

Ligand binding site composition:

B-Factor:	13.140
Number of residues:	45
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.017	877.500

% Hydrophobic	% Polar
41.54	58.46
According to VolSite

Ligand :

HET Code:	G05
Formula:	C29H40N2O8S
Molecular weight:	576.701 g/mol
DrugBank ID:	-
Buried Surface Area:	68.16 %
Polar Surface area:	132.01 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	2
Rings:	4
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
15.7516	22.6351	16.7762

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	4.24	0	Hydrophobic	false
C16	CB	ALA- 28	4.22	0	Hydrophobic	false
C6	CB	ALA- 28	3.54	0	Hydrophobic	false
C40	CB	ASP- 29	4.02	0	Hydrophobic	false
O39	N	ASP- 30	3.31	136.1	H-Bond (Protein Donor)	false
C40	CB	ASP- 30	3.94	0	Hydrophobic	false
C7	CG2	VAL- 32	3.8	0	Hydrophobic	false
C2	CD1	ILE- 47	4.36	0	Hydrophobic	false
C40	CG2	ILE- 47	3.92	0	Hydrophobic	false
C3	CB	ILE- 47	4.24	0	Hydrophobic	false
C24	CD1	ILE- 50	4.08	0	Hydrophobic	false
C36	CG	PRO- 81	3.63	0	Hydrophobic	false
C34	CG1	VAL- 82	3.6	0	Hydrophobic	false
C6	CD1	ILE- 84	4.36	0	Hydrophobic	false
C37	CD1	ILE- 84	3.97	0	Hydrophobic	false
C15	CD2	LEU- 123	3.85	0	Hydrophobic	false
O18	OD1	ASP- 125	2.68	157.91	H-Bond (Protein Donor)	false
N20	O	GLY- 127	3.21	161.76	H-Bond (Ligand Donor)	false
C25	CB	ALA- 128	3.98	0	Hydrophobic	false
C26	CB	ASP- 129	4.28	0	Hydrophobic	false
C28	CB	ASP- 129	3.74	0	Hydrophobic	false
O27	N	ASP- 129	2.95	164.6	H-Bond (Protein Donor)	false
C25	CB	ASP- 130	4.28	0	Hydrophobic	false
C25	CG2	VAL- 132	4.39	0	Hydrophobic	false
C31	CB	ILE- 147	3.97	0	Hydrophobic	false
C37	CB	ILE- 150	4.36	0	Hydrophobic	false
C5	CD1	ILE- 150	4.04	0	Hydrophobic	false
C15	CG1	VAL- 182	3.87	0	Hydrophobic	false
C14	CD1	ILE- 184	4.33	0	Hydrophobic	false
C24	CD1	ILE- 184	4.29	0	Hydrophobic	false
C15	CG2	ILE- 184	4.07	0	Hydrophobic	false
O23	O	HOH- 1144	3.47	135.37	H-Bond (Protein Donor)	false