scPDB - 1d4k entry

Protein Data Bank Entry:

PDB ID : 1d4k

Resolution :1.850 Å

Experimental Method : X-ray

Deposition Date : 1999-10-04

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_HV1A2
AC:	P03369
Organism:	Human immunodeficiency virus type 1 group M subtype B
Reign:	Viruses
TaxID:	11685
EC Number:	3.4.23.16

Chains:

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

Ligand binding site composition:

B-Factor:	19.361
Number of residues:	41
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.824	749.250

% Hydrophobic	% Polar
43.24	56.76
According to VolSite

Ligand :

HET Code:	PI8
Formula:	C41H55N4O6
Molecular weight:	699.899 g/mol
DrugBank ID:	-
Buried Surface Area:	60.49 %
Polar Surface area:	153.6 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	6
Rings:	6
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
5.07863	-2.43625	14.6772

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
C14	CD2	LEU- 23	3.8	0	Hydrophobic	false
C23	CD2	LEU- 23	4.26	0	Hydrophobic	false
C25	CD2	LEU- 23	4.1	0	Hydrophobic	false
O3	OD2	ASP- 25	2.7	159.47	H-Bond (Ligand Donor)	false
N2	OD2	ASP- 25	2.91	144.9	H-Bond (Ligand Donor)	false
N2	OD2	ASP- 25	2.91	0	Ionic (Ligand Cationic)	false
N1	O	GLY- 27	3.29	139.76	H-Bond (Ligand Donor)	false
N3	O	GLY- 27	3.29	158.7	H-Bond (Ligand Donor)	false
C34	CB	ALA- 28	3.92	0	Hydrophobic	false
C5	CB	ALA- 28	3.64	0	Hydrophobic	false
O1	N	ASP- 29	3.3	160.43	H-Bond (Protein Donor)	false
O5	N	ASP- 29	2.78	173.11	H-Bond (Protein Donor)	false
O1	OD2	ASP- 29	2.98	167.76	H-Bond (Ligand Donor)	false
C9	CB	ASP- 29	4.25	0	Hydrophobic	false
C7	CB	ASP- 30	4.02	0	Hydrophobic	false
C6	CG2	VAL- 32	3.25	0	Hydrophobic	false
C33	CD1	ILE- 47	3.93	0	Hydrophobic	false
C6	CD1	ILE- 47	4.06	0	Hydrophobic	false
N4	O	GLY- 48	3.42	150.59	H-Bond (Ligand Donor)	false
C23	CD1	ILE- 50	4.47	0	Hydrophobic	false
C35	CD1	ILE- 50	3.66	0	Hydrophobic	false
C4	CG1	ILE- 50	3.95	0	Hydrophobic	false
C17	CG	PRO- 81	3.88	0	Hydrophobic	false
C28	CB	PRO- 81	3.56	0	Hydrophobic	false
C25	CG1	VAL- 82	3.62	0	Hydrophobic	false
C14	CG1	VAL- 82	3.64	0	Hydrophobic	false
C5	CD1	ILE- 84	4.37	0	Hydrophobic	false
C12	CD1	ILE- 84	3.69	0	Hydrophobic	false
C19	CD1	ILE- 84	4.4	0	Hydrophobic	false
C23	CD1	ILE- 84	3.67	0	Hydrophobic	false
C35	CD1	ILE- 84	3.39	0	Hydrophobic	false