scPDB - 3dcr entry

Protein Data Bank Entry:

PDB ID : 3dcr

Resolution :1.400 Å

Experimental Method : X-ray

Deposition Date : 2008-06-04

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	47 %
B	53 %

Ligand binding site composition:

B-Factor:	13.910
Number of residues:	47
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	2
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.081	779.625

% Hydrophobic	% Polar
42.86	57.14
According to VolSite

Ligand :

HET Code:	KVS
Formula:	C36H67N10O10
Molecular weight:	799.978 g/mol
DrugBank ID:	-
Buried Surface Area:	59.76 %
Polar Surface area:	356.01 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	13
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
-4.98793	-0.828643	-13.509

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
CX	CD2	LEU- 23	3.94	0	Hydrophobic	false
CG	CD2	LEU- 23	3.93	0	Hydrophobic	false
OA	OD2	ASP- 25	2.58	161.66	H-Bond (Ligand Donor)	false
OB	OD2	ASP- 25	2.7	160.32	H-Bond (Ligand Donor)	false
OA	OD1	ASP- 25	2.66	148.48	H-Bond (Protein Donor)	false
N3	O	GLY- 27	2.93	158.09	H-Bond (Ligand Donor)	false
N4	O	GLY- 27	3.04	161.5	H-Bond (Ligand Donor)	false
CG3	CB	ALA- 28	4.14	0	Hydrophobic	false
CD1	CB	ALA- 28	4.14	0	Hydrophobic	false
CB3	CB	ALA- 28	3.81	0	Hydrophobic	false
O1	N	ASP- 29	2.89	165.66	H-Bond (Protein Donor)	false
O4	N	ASP- 29	3.05	164.05	H-Bond (Protein Donor)	false
CB	CB	ASP- 29	4.21	0	Hydrophobic	false
NE5	OD2	ASP- 29	2.76	154.17	H-Bond (Ligand Donor)	false
NH2	OD1	ASP- 29	3.45	126.41	H-Bond (Ligand Donor)	false
NH2	OD2	ASP- 29	3.44	131.96	H-Bond (Ligand Donor)	false
CZ1	OD1	ASP- 29	3.93	0	Ionic (Ligand Cationic)	false
CZ1	OD2	ASP- 29	3.58	0	Ionic (Ligand Cationic)	false
CD1	CB	ASP- 30	3.94	0	Hydrophobic	false
OE1	N	ASP- 30	2.87	154.13	H-Bond (Protein Donor)	false
NE2	OD2	ASP- 30	2.84	172.6	H-Bond (Ligand Donor)	false
CG3	CG2	VAL- 32	4.46	0	Hydrophobic	false
CG4	CG2	VAL- 32	4.22	0	Hydrophobic	false
CD1	CG2	VAL- 32	4.19	0	Hydrophobic	false
CG1	CD1	ILE- 47	3.93	0	Hydrophobic	false
CG4	CD1	ILE- 47	4.04	0	Hydrophobic	false
N1	O	GLY- 48	3.02	124.85	H-Bond (Ligand Donor)	false
N2	O	GLY- 48	2.98	157.95	H-Bond (Ligand Donor)	false
N5	O	GLY- 48	2.92	166.31	H-Bond (Ligand Donor)	false
O5	N	GLY- 48	2.9	170.02	H-Bond (Protein Donor)	false
CB1	CG2	ILE- 50	4.24	0	Hydrophobic	false
CG3	CG1	ILE- 50	4.18	0	Hydrophobic	false
CE	CG1	ILE- 50	3.95	0	Hydrophobic	false
CY	CD1	ILE- 50	4.48	0	Hydrophobic	false
CG4	CD1	ILE- 50	3.81	0	Hydrophobic	false
CH3	CB	PRO- 81	3.87	0	Hydrophobic	false
CE	CG	PRO- 81	4.38	0	Hydrophobic	false
CY	CG	PRO- 81	4.31	0	Hydrophobic	false
CG	CB	VAL- 82	4.27	0	Hydrophobic	false
CD2	CG2	VAL- 82	4.2	0	Hydrophobic	false
CE	CB	VAL- 82	4.32	0	Hydrophobic	false
CG3	CD1	ILE- 84	3.85	0	Hydrophobic	false
CE	CG2	ILE- 84	4.23	0	Hydrophobic	false
CY	CD1	ILE- 84	4.2	0	Hydrophobic	false
CB2	CG2	ILE- 84	3.97	0	Hydrophobic	false
CL	CD1	ILE- 84	3.83	0	Hydrophobic	false
CB3	CD1	ILE- 84	4.15	0	Hydrophobic	false