scPDB - 1tcw entry

Protein Data Bank Entry:

PDB ID : 1tcw

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 1996-06-05

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_SIVM1
AC:	P05896
Organism:	Simian immunodeficiency virus
Reign:	Viruses
TaxID:	11733
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	74 %
B	26 %

Ligand binding site composition:

B-Factor:	6.712
Number of residues:	28
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.857	664.875

% Hydrophobic	% Polar
41.62	58.38
According to VolSite

Ligand :

HET Code:	IM1
Formula:	C31H42N4O4
Molecular weight:	534.690 g/mol
DrugBank ID:	-
Buried Surface Area:	45.43 %
Polar Surface area:	116.34 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	4
Rings:	3
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	14

Mass center Coordinates

X	Y	Z
62.3084	19.1491	24.3991

Binding mode :

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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
DuAr	CZ	ARG- 8	3.78	149.24	Pi/Cation	false
C25	CD	ARG- 8	3.5	0	Hydrophobic	false
C26	CD1	LEU- 23	3.48	0	Hydrophobic	false
C33	CB	ALA- 28	3.66	0	Hydrophobic	false
C4	CB	ASP- 29	4.4	0	Hydrophobic	false
O29	N	ASP- 29	2.99	164.43	H-Bond (Protein Donor)	false
C34	CB	ASP- 30	3.83	0	Hydrophobic	false
C33	CD1	ILE- 32	3.46	0	Hydrophobic	false
C17	CB	VAL- 47	4.1	0	Hydrophobic	false
C32	CG2	VAL- 47	4.06	0	Hydrophobic	false
C34	CB	VAL- 47	3.92	0	Hydrophobic	false
O18	N	GLY- 48	2.73	155.24	H-Bond (Protein Donor)	false
N30	O	GLY- 48	2.95	148.01	H-Bond (Ligand Donor)	false
C33	CD1	ILE- 50	4.45	0	Hydrophobic	false
C27	CD1	ILE- 82	4.11	0	Hydrophobic	false
C25	CG2	ILE- 82	4.02	0	Hydrophobic	false
C33	CD1	ILE- 84	3.49	0	Hydrophobic	false