scPDB - 1d4i entry

Protein Data Bank Entry:

PDB ID : 1d4i

Resolution :1.810 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_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	49 %
B	51 %

Ligand binding site composition:

B-Factor:	15.557
Number of residues:	45
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.780	749.250

% Hydrophobic	% Polar
47.30	52.70
According to VolSite

Ligand :

HET Code:	BEG
Formula:	C38H40N2O7
Molecular weight:	636.733 g/mol
DrugBank ID:	DB04190
Buried Surface Area:	71.44 %
Polar Surface area:	137.35 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	5
Rings:	6
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
13.0177	22.9122	5.55638

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	3.78	0	Hydrophobic	false
C13	CD2	LEU- 23	4.46	0	Hydrophobic	false
O24	OD1	ASP- 25	2.65	138.74	H-Bond (Ligand Donor)	false
O24	OD2	ASP- 25	2.92	149.75	H-Bond (Ligand Donor)	false
N21	O	GLY- 27	3.2	162.62	H-Bond (Ligand Donor)	false
C42	CB	ALA- 28	3.57	0	Hydrophobic	false
O45	OD2	ASP- 29	3.25	163.98	H-Bond (Ligand Donor)	false
O45	N	ASP- 29	3.13	158.55	H-Bond (Protein Donor)	false
C47	CB	ASP- 29	4.31	0	Hydrophobic	false
C46	CB	ASP- 30	4.03	0	Hydrophobic	false
C42	CG1	VAL- 32	3.8	0	Hydrophobic	false
C40	CB	ILE- 47	4.46	0	Hydrophobic	false
C46	CG2	ILE- 47	4.15	0	Hydrophobic	false
C43	CD1	ILE- 47	3.92	0	Hydrophobic	false
C31	CG1	ILE- 50	4.33	0	Hydrophobic	false
C09	CB	PRO- 81	4.05	0	Hydrophobic	false
C07	CG1	VAL- 82	3.69	0	Hydrophobic	false
C12	CG1	VAL- 82	3.64	0	Hydrophobic	false
C42	CD1	ILE- 84	4.36	0	Hydrophobic	false
C13	CD1	ILE- 84	3.44	0	Hydrophobic	false
C02	CD1	LEU- 123	3.67	0	Hydrophobic	false
N27	O	GLY- 127	3.11	166.32	H-Bond (Ligand Donor)	false
O35	O	GLY- 127	3.25	139.1	H-Bond (Ligand Donor)	false
C32	CB	ALA- 128	3.56	0	Hydrophobic	false
O35	N	ASP- 129	3.08	153.75	H-Bond (Protein Donor)	false
C37	CB	ASP- 129	4.13	0	Hydrophobic	false
C36	CB	ASP- 130	3.72	0	Hydrophobic	false
C32	CG1	VAL- 132	3.87	0	Hydrophobic	false
C30	CB	ILE- 147	4.32	0	Hydrophobic	false
C36	CG2	ILE- 147	3.94	0	Hydrophobic	false
C33	CD1	ILE- 147	3.93	0	Hydrophobic	false
C08	CG2	ILE- 150	4.16	0	Hydrophobic	false
C13	CG2	ILE- 150	4.38	0	Hydrophobic	false
C41	CD1	ILE- 150	4.02	0	Hydrophobic	false
C06	CG	PRO- 181	4.46	0	Hydrophobic	false
C05	CB	PRO- 181	3.69	0	Hydrophobic	false
C01	CG2	VAL- 182	3.72	0	Hydrophobic	false
C02	CG2	VAL- 182	3.67	0	Hydrophobic	false
C32	CD1	ILE- 184	4.5	0	Hydrophobic	false
C23	CD1	ILE- 184	3.55	0	Hydrophobic	false