scPDB - 1mes entry

Protein Data Bank Entry:

PDB ID : 1mes

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 1997-04-11

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	50 %
B	50 %

Ligand binding site composition:

B-Factor:	21.035
Number of residues:	42
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.950	779.625

% Hydrophobic	% Polar
47.19	52.81
According to VolSite

Ligand :

HET Code:	DMP
Formula:	C35H38N2O5
Molecular weight:	566.687 g/mol
DrugBank ID:	-
Buried Surface Area:	67.38 %
Polar Surface area:	104.47 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	4
Rings:	5
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
-9.41164	16.3095	27.9446

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
O4	OD2	ASP- 25	3.43	130.39	H-Bond (Ligand Donor)	false
O4	OD1	ASP- 25	2.95	159.87	H-Bond (Ligand Donor)	false
O5	OD1	ASP- 25	2.79	155.74	H-Bond (Ligand Donor)	false
C74	CB	ALA- 28	4.09	0	Hydrophobic	false
C75	CB	ALA- 28	3.58	0	Hydrophobic	false
C23	CB	ALA- 28	3.41	0	Hydrophobic	false
C27	CB	ASP- 30	3.8	0	Hydrophobic	false
C77	CB	ASP- 30	3.87	0	Hydrophobic	false
O27	N	ASP- 30	2.97	149.17	H-Bond (Protein Donor)	false
O77	N	ASP- 30	3.09	144.47	H-Bond (Protein Donor)	false
C27	CG2	VAL- 32	3.55	0	Hydrophobic	false
C75	CG1	VAL- 32	3.8	0	Hydrophobic	false
C74	CD1	ILE- 47	4.01	0	Hydrophobic	false
C24	CD1	ILE- 47	4.23	0	Hydrophobic	false
O1	N	ILE- 50	3.3	150.31	H-Bond (Protein Donor)	false
O1	N	ILE- 50	3.23	156.92	H-Bond (Protein Donor)	false
C22	CD1	ILE- 50	3.56	0	Hydrophobic	false
C32	CG1	ILE- 50	3.78	0	Hydrophobic	false
C62	CG1	ILE- 50	3.97	0	Hydrophobic	false
C76	CD1	ILE- 50	3.59	0	Hydrophobic	false
C33	CG	PRO- 81	3.27	0	Hydrophobic	false
C63	CG	PRO- 81	3.55	0	Hydrophobic	false
C33	CG2	VAL- 82	3.83	0	Hydrophobic	false
C63	CG1	VAL- 82	3.6	0	Hydrophobic	false
C23	CG1	VAL- 84	3.98	0	Hydrophobic	false
C30	CG1	VAL- 84	4.37	0	Hydrophobic	false
C60	CG2	VAL- 84	4.34	0	Hydrophobic	false
C75	CG2	VAL- 84	4.12	0	Hydrophobic	false