scPDB - 1tcx entry

Protein Data Bank Entry:

PDB ID : 1tcx

Resolution :2.300 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_HV1B5
AC:	P04587
Organism:	Human immunodeficiency virus type 1 group M subtype B
Reign:	Viruses
TaxID:	11682
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:	13.737
Number of residues:	38
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.646	762.750

% Hydrophobic	% Polar
40.71	59.29
According to VolSite

Ligand :

HET Code:	IM1
Formula:	C31H42N4O4
Molecular weight:	534.690 g/mol
DrugBank ID:	-
Buried Surface Area:	67.38 %
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
12.5314	23.6591	5.50077

Binding mode :

What is Poseview ?

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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
C12	CD2	LEU- 23	3.96	0	Hydrophobic	false
C27	CD2	LEU- 23	3.73	0	Hydrophobic	false
O18	OD1	ASP- 25	2.83	132.13	H-Bond (Ligand Donor)	false
O18	OD2	ASP- 25	2.84	161.55	H-Bond (Ligand Donor)	false
N8	O	GLY- 27	2.94	163.22	H-Bond (Ligand Donor)	false
N30	O	GLY- 27	3.17	159.26	H-Bond (Ligand Donor)	false
C34	CB	ALA- 28	3.91	0	Hydrophobic	false
C4	CB	ALA- 28	3.96	0	Hydrophobic	false
N36	N	ASP- 29	3.21	173.23	H-Bond (Protein Donor)	false
C33	CD1	ILE- 32	3.48	0	Hydrophobic	false
C4	CD1	ILE- 32	3.67	0	Hydrophobic	false
C3	CG1	VAL- 47	3.81	0	Hydrophobic	false
C33	CG1	VAL- 47	3.37	0	Hydrophobic	false
N39	O	GLY- 48	2.84	142.76	H-Bond (Ligand Donor)	false
C3	CG2	ILE- 50	4.19	0	Hydrophobic	false
C4	CD1	ILE- 50	4.18	0	Hydrophobic	false
C34	CD1	ILE- 50	4.38	0	Hydrophobic	false
C16	CD1	ILE- 50	3.91	0	Hydrophobic	false
C15	CG	PRO- 81	3.45	0	Hydrophobic	false
C24	CG	PRO- 81	3.73	0	Hydrophobic	false
C14	CG2	ILE- 82	3.63	0	Hydrophobic	false
C27	CG2	ILE- 82	4	0	Hydrophobic	false
C4	CD1	ILE- 84	4	0	Hydrophobic	false
C21	CD1	ILE- 84	3.89	0	Hydrophobic	false
C34	CD1	ILE- 84	4.16	0	Hydrophobic	false
C10	CD1	ILE- 84	3.9	0	Hydrophobic	false