scPDB - 1d4j entry

Protein Data Bank Entry:

PDB ID : 1d4j

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	48 %
B	52 %

Ligand binding site composition:

B-Factor:	21.142
Number of residues:	46
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.889	725.625

% Hydrophobic	% Polar
45.58	54.42
According to VolSite

Ligand :

HET Code:	MSC
Formula:	C36H36ClFN2O7
Molecular weight:	663.132 g/mol
DrugBank ID:	-
Buried Surface Area:	71.65 %
Polar Surface area:	137.35 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	5
Rings:	5
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	14

Mass center Coordinates

X	Y	Z
13.0509	22.9291	5.49365

Binding mode :

What is Poseview ?

2D View
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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
C11	CD2	LEU- 23	3.53	0	Hydrophobic	false
O32	OD1	ASP- 25	2.63	125.44	H-Bond (Ligand Donor)	false
O32	OD2	ASP- 25	2.82	153.67	H-Bond (Ligand Donor)	false
CL	CB	ALA- 28	3.57	0	Hydrophobic	false
C51	CB	ALA- 28	4.04	0	Hydrophobic	false
C48	CB	ASP- 29	4.22	0	Hydrophobic	false
C49	CB	ASP- 30	3.86	0	Hydrophobic	false
CL	CG1	VAL- 32	4.29	0	Hydrophobic	false
C47	CB	ILE- 47	4.46	0	Hydrophobic	false
C50	CD1	ILE- 47	4.27	0	Hydrophobic	false
C49	CG2	ILE- 47	4.12	0	Hydrophobic	false
C17	CG1	ILE- 50	4.25	0	Hydrophobic	false
C49	CD1	LEU- 76	4.35	0	Hydrophobic	false
C08	CB	PRO- 81	4.28	0	Hydrophobic	false
C11	CG1	VAL- 82	3.67	0	Hydrophobic	false
CL	CD1	ILE- 84	3.86	0	Hydrophobic	false
C05	CD1	ILE- 84	3.41	0	Hydrophobic	false
C35	CD2	LEU- 123	3.66	0	Hydrophobic	false
O02	OD2	ASP- 125	2.71	156.64	H-Bond (Ligand Donor)	false
N14	O	GLY- 127	3.02	173.18	H-Bond (Ligand Donor)	false
O24	O	GLY- 127	3.06	152.34	H-Bond (Ligand Donor)	false
C18	CB	ALA- 128	3.57	0	Hydrophobic	false
C22	CB	ASP- 129	4.08	0	Hydrophobic	false
C21	CB	ASP- 129	4.42	0	Hydrophobic	false
O24	N	ASP- 129	3.04	151.18	H-Bond (Protein Donor)	false
C19	CB	ASP- 130	3.75	0	Hydrophobic	false
C18	CG1	VAL- 132	3.76	0	Hydrophobic	false
C20	CG2	ILE- 147	3.88	0	Hydrophobic	false
C21	CB	ILE- 147	4.26	0	Hydrophobic	false
C19	CD1	ILE- 147	3.84	0	Hydrophobic	false
C05	CG2	ILE- 150	4.18	0	Hydrophobic	false
C07	CG2	ILE- 150	4.26	0	Hydrophobic	false
C46	CD1	ILE- 150	4.4	0	Hydrophobic	false
CL	CG2	ILE- 150	4.07	0	Hydrophobic	false
C40	CB	PRO- 181	3.6	0	Hydrophobic	false
C36	CG2	VAL- 182	3.62	0	Hydrophobic	false
C37	CG2	VAL- 182	3.75	0	Hydrophobic	false
C35	CD1	ILE- 184	3.71	0	Hydrophobic	false
N44	O	HOH- 301	2.91	138.18	H-Bond (Ligand Donor)	false