scPDB - 1npa entry

Protein Data Bank Entry:

PDB ID : 1npa

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2003-01-17

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_HV1B1
AC:	P03366
Organism:	Human immunodeficiency virus type 1 group M subtype B
Reign:	Viruses
TaxID:	11678
EC Number:	3.4.23.16

Chains:

Chain Name:	Percentage of Residues within binding site
A	52 %
B	48 %

Ligand binding site composition:

B-Factor:	14.706
Number of residues:	43
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.062	799.875

% Hydrophobic	% Polar
47.26	52.74
According to VolSite

Ligand :

HET Code:	3NH
Formula:	C36H45N3O7
Molecular weight:	631.758 g/mol
DrugBank ID:	DB01824
Buried Surface Area:	70.83 %
Polar Surface area:	158.56 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	5
Rings:	6
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	2
Rule of Five Violation:	1
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
12.2192	23.8838	5.49637

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
C12	CD2	LEU- 23	3.81	0	Hydrophobic	false
C42	CD2	LEU- 23	3.74	0	Hydrophobic	false
N29	OD1	ASP- 25	3.06	137.27	H-Bond (Ligand Donor)	false
O07	OD2	ASP- 25	3.29	126.87	H-Bond (Ligand Donor)	false
O07	OD1	ASP- 25	2.59	166.74	H-Bond (Ligand Donor)	false
O07	OD2	ASP- 25	2.63	164.8	H-Bond (Protein Donor)	false
NP4	O	GLY- 27	3.27	171.79	H-Bond (Ligand Donor)	false
C47	CB	ALA- 28	4.08	0	Hydrophobic	false
C27	CB	ALA- 28	3.54	0	Hydrophobic	false
O2	N	ASP- 29	3.23	145.97	H-Bond (Protein Donor)	false
O46	N	ASP- 30	3.21	157.24	H-Bond (Protein Donor)	false
C47	CB	ASP- 30	3.84	0	Hydrophobic	false
C25	CB	ASP- 30	4.09	0	Hydrophobic	false
C27	CG2	VAL- 32	4.29	0	Hydrophobic	false
C25	CG2	VAL- 32	3.22	0	Hydrophobic	false
C47	CG2	VAL- 32	3.41	0	Hydrophobic	false
C45	CB	ILE- 47	4.5	0	Hydrophobic	false
C22	CB	ILE- 47	4.21	0	Hydrophobic	false
C24	CD1	ILE- 47	3.94	0	Hydrophobic	false
C47	CD1	ILE- 47	4.07	0	Hydrophobic	false
O18	N	ILE- 50	3.5	150.01	H-Bond (Protein Donor)	false
C48	CG1	ILE- 50	4.3	0	Hydrophobic	false
C38	CG1	ILE- 50	4.27	0	Hydrophobic	false
C27	CG1	ILE- 50	4.14	0	Hydrophobic	false
C16	CG	PRO- 81	3.95	0	Hydrophobic	false
C39	CG	PRO- 81	4.03	0	Hydrophobic	false
C40	CB	PRO- 81	4.4	0	Hydrophobic	false
C15	CB	PRO- 81	3.57	0	Hydrophobic	false
C13	CG2	VAL- 82	3.72	0	Hydrophobic	false
C41	CG1	VAL- 82	3.6	0	Hydrophobic	false
C26	CG2	ILE- 84	3.99	0	Hydrophobic	false
C10	CD1	ILE- 84	3.4	0	Hydrophobic	false
C38	CD1	ILE- 84	3.77	0	Hydrophobic	false
O01	O	HOH- 336	3.2	147.38	H-Bond (Protein Donor)	false