scPDB - 1ivp entry

Protein Data Bank Entry:

PDB ID : 1ivp

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 1993-03-18

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_HV2RO
AC:	P04584
Organism:	Human immunodeficiency virus type 2 subtype A
Reign:	Viruses
TaxID:	11720
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	12.602
Number of residues:	43
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.248	985.500

% Hydrophobic	% Polar
46.23	53.77
According to VolSite

Ligand :

HET Code:	1ZK
Formula:	C45H61N7O7
Molecular weight:	812.009 g/mol
DrugBank ID:	-
Buried Surface Area:	56.42 %
Polar Surface area:	207.65 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	7
Rings:	5
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	21

Mass center Coordinates

X	Y	Z
1.21093	16.4195	20.871

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
CD21	CD2	LEU- 23	3.75	0	Hydrophobic	false
CG2	CD2	LEU- 23	4.14	0	Hydrophobic	false
OB1	OD1	ASP- 25	3.39	163.07	H-Bond (Ligand Donor)	false
N1	O	GLY- 27	3.11	169.17	H-Bond (Ligand Donor)	false
N2	O	GLY- 27	3.04	135.92	H-Bond (Ligand Donor)	false
CB	CB	ALA- 28	4.48	0	Hydrophobic	false
CB2	CB	ALA- 28	4.39	0	Hydrophobic	false
O	N	ASP- 29	2.93	145.77	H-Bond (Protein Donor)	false
O4	N	ASP- 29	3.1	140.57	H-Bond (Protein Donor)	false
NE2	N	ASP- 30	3.45	129.52	H-Bond (Protein Donor)	false
CG12	CB	ASP- 30	4.38	0	Hydrophobic	false
CB	CG2	VAL- 47	4.37	0	Hydrophobic	false
CD11	CB	VAL- 47	4.1	0	Hydrophobic	false
N	O	GLY- 48	3.25	132.66	H-Bond (Ligand Donor)	false
ND1	O	GLY- 48	3.25	158.24	H-Bond (Ligand Donor)	false
CD1	CG1	ILE- 50	3.82	0	Hydrophobic	false
CG11	CG2	ILE- 50	3.97	0	Hydrophobic	false
C1A	CG	PRO- 81	4.39	0	Hydrophobic	false
C5	CB	PRO- 81	3.55	0	Hydrophobic	false
C6	CG	PRO- 81	3.95	0	Hydrophobic	false
CE11	CG	PRO- 81	3.46	0	Hydrophobic	false
CE2	CD1	ILE- 82	3.82	0	Hydrophobic	false
CZ	CB	ILE- 82	3.44	0	Hydrophobic	false
CG11	CG2	ILE- 82	4.46	0	Hydrophobic	false
CG2	CG2	ILE- 82	4.02	0	Hydrophobic	false
C2	CD1	ILE- 82	3.29	0	Hydrophobic	false
C3	CD1	ILE- 82	3.55	0	Hydrophobic	false
CB1	CD1	ILE- 84	4.33	0	Hydrophobic	false
CG21	CD1	ILE- 84	3.59	0	Hydrophobic	false
CG11	CD1	ILE- 84	3.59	0	Hydrophobic	false
CD21	CG2	ILE- 84	3.81	0	Hydrophobic	false