scPDB - 3dck entry

Protein Data Bank Entry:

PDB ID : 3dck

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2008-06-03

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Protease
ID:	O38732_9HIV1
AC:	O38732
Organism:	Human immunodeficiency virus 1
Reign:	Viruses
TaxID:	11676
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	49 %
B	51 %

Ligand binding site composition:

B-Factor:	21.913
Number of residues:	47
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	2
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.908	816.750

% Hydrophobic	% Polar
40.91	59.09
According to VolSite

Ligand :

HET Code:	KVI
Formula:	C36H67N10O9
Molecular weight:	783.979 g/mol
DrugBank ID:	-
Buried Surface Area:	57.08 %
Polar Surface area:	332.61 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	11
Rings:	0
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	30

Mass center Coordinates

X	Y	Z
-5.03242	-1.19218	-13.0101

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
C22	CD2	LEU- 23	4.34	0	Hydrophobic	false
C29	CD2	LEU- 23	4.44	0	Hydrophobic	false
O6	ND2	ASN- 25	2.87	163.73	H-Bond (Protein Donor)	false
N9	O	GLY- 27	2.79	153.08	H-Bond (Ligand Donor)	false
N6	O	GLY- 27	3	154.17	H-Bond (Ligand Donor)	false
C18	CB	ALA- 28	4.23	0	Hydrophobic	false
C19	CB	ALA- 28	3.93	0	Hydrophobic	false
C11	CB	ALA- 28	3.86	0	Hydrophobic	false
O8	N	ASP- 29	2.97	167.86	H-Bond (Protein Donor)	false
O3	N	ASP- 29	3.14	161.97	H-Bond (Protein Donor)	false
C35	CB	ASP- 29	4.2	0	Hydrophobic	false
N5	OD2	ASP- 29	3	161.18	H-Bond (Ligand Donor)	false
C19	CB	ASP- 30	3.86	0	Hydrophobic	false
O4	N	ASP- 30	2.81	157.85	H-Bond (Protein Donor)	false
N7	OD2	ASP- 30	2.74	168.04	H-Bond (Ligand Donor)	false
C18	CG2	VAL- 32	4.3	0	Hydrophobic	false
C12	CG2	VAL- 32	4.18	0	Hydrophobic	false
C19	CG2	VAL- 32	4.16	0	Hydrophobic	false
C12	CD1	ILE- 47	3.96	0	Hydrophobic	false
C17	CD1	ILE- 47	3.93	0	Hydrophobic	false
N8	O	GLY- 48	2.82	155.55	H-Bond (Ligand Donor)	false
N1	O	GLY- 48	3.03	155.15	H-Bond (Ligand Donor)	false
O1	N	GLY- 48	3.04	177.75	H-Bond (Protein Donor)	false
C16	CG2	ILE- 50	4.48	0	Hydrophobic	false
C18	CD1	ILE- 50	4.2	0	Hydrophobic	false
C24	CG1	ILE- 50	3.94	0	Hydrophobic	false
C31	CD1	ILE- 50	4.3	0	Hydrophobic	false
C12	CD1	ILE- 50	3.72	0	Hydrophobic	false
C8	CB	PRO- 81	4.08	0	Hydrophobic	false
C31	CG	PRO- 81	4.27	0	Hydrophobic	false
C24	CG	PRO- 81	3.69	0	Hydrophobic	false
C22	CB	VAL- 82	4.1	0	Hydrophobic	false
C23	CG2	VAL- 82	3.99	0	Hydrophobic	false
C24	CB	VAL- 82	4.15	0	Hydrophobic	false
C31	CG2	VAL- 82	4.49	0	Hydrophobic	false
C18	CD1	ILE- 84	3.91	0	Hydrophobic	false
C24	CG2	ILE- 84	4.42	0	Hydrophobic	false
C28	CD1	ILE- 84	3.9	0	Hydrophobic	false
C31	CD1	ILE- 84	4.17	0	Hydrophobic	false
C21	CG2	ILE- 84	4.02	0	Hydrophobic	false
C11	CD1	ILE- 84	3.94	0	Hydrophobic	false