scPDB - 1d4s entry

Protein Data Bank Entry:

PDB ID : 1d4s

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 1999-10-05

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_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	56 %
B	44 %

Ligand binding site composition:

B-Factor:	17.620
Number of residues:	43
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.783	853.875

% Hydrophobic	% Polar
40.71	59.29
According to VolSite

Ligand :

HET Code:	TPV
Formula:	C31H32F3N2O5S
Molecular weight:	601.656 g/mol
DrugBank ID:	DB00932
Buried Surface Area:	64.8 %
Polar Surface area:	116.8 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	1
Rings:	4
Aromatic rings:	3
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
11.8573	24.4472	5.75726

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
F41	CD	ARG- 8	3.25	0	Hydrophobic	false
C22	CD2	LEU- 23	4.22	0	Hydrophobic	false
C14	CD2	LEU- 23	4.24	0	Hydrophobic	false
C19	CD2	LEU- 23	3.3	0	Hydrophobic	false
F40	CD2	LEU- 23	3.42	0	Hydrophobic	false
O8	OD2	ASP- 25	3.19	158.43	H-Bond (Ligand Donor)	false
C11	CB	ALA- 28	3.5	0	Hydrophobic	false
C25	CB	ALA- 28	3.51	0	Hydrophobic	false
N34	N	ASP- 29	2.99	171.18	H-Bond (Protein Donor)	false
O31	N	ASP- 30	3.01	149.7	H-Bond (Protein Donor)	false
C26	CG2	VAL- 32	3.77	0	Hydrophobic	false
C26	CD1	ILE- 47	4.09	0	Hydrophobic	false
O7	N	ILE- 50	2.87	143.52	H-Bond (Protein Donor)	false
O7	N	ILE- 50	3.29	164.39	H-Bond (Protein Donor)	false
C11	CG1	ILE- 50	4.22	0	Hydrophobic	false
C22	CD1	ILE- 50	4.45	0	Hydrophobic	false
C25	CG1	ILE- 50	3.84	0	Hydrophobic	false
C15	CD1	ILE- 50	3.78	0	Hydrophobic	false
C15	CG	PRO- 81	3.77	0	Hydrophobic	false
C17	CD1	PHE- 82	3.3	0	Hydrophobic	false
F42	CB	PHE- 82	3.84	0	Hydrophobic	false
C16	CB	PHE- 82	3.33	0	Hydrophobic	false
C13	CG2	VAL- 84	4.45	0	Hydrophobic	false
C22	CG2	VAL- 84	3.71	0	Hydrophobic	false
C25	CG1	VAL- 84	4.17	0	Hydrophobic	false