scPDB - 1mer entry

Protein Data Bank Entry:

PDB ID : 1mer

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:	20.173
Number of residues:	42
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.725	658.125

% Hydrophobic	% Polar
42.05	57.95
According to VolSite

Ligand :

HET Code:	DMQ
Formula:	C33H36N4O3
Molecular weight:	536.664 g/mol
DrugBank ID:	DB02102
Buried Surface Area:	70.83 %
Polar Surface area:	116.05 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:	8

Mass center Coordinates

X	Y	Z
-9.4474	16.403	27.9109

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
C37	CD2	LEU- 23	4.46	0	Hydrophobic	false
C63	CD2	LEU- 23	4.29	0	Hydrophobic	false
O4	OD1	ASP- 25	3.3	124.58	H-Bond (Ligand Donor)	false
O4	OD2	ASP- 25	2.95	175.56	H-Bond (Ligand Donor)	false
O5	OD1	ASP- 25	2.88	158.95	H-Bond (Ligand Donor)	false
O5	OD2	ASP- 25	3.42	122.91	H-Bond (Ligand Donor)	false
C23	CB	ALA- 28	3.51	0	Hydrophobic	false
C78	CB	ALA- 28	3.58	0	Hydrophobic	false
C23	CB	ASP- 30	4.34	0	Hydrophobic	false
C77	CB	ASP- 30	4.24	0	Hydrophobic	false
N79	OD2	ASP- 30	2.91	150.89	H-Bond (Ligand Donor)	false
C23	CG2	VAL- 32	3.86	0	Hydrophobic	false
C78	CG1	VAL- 32	3.63	0	Hydrophobic	false
C23	CD1	ILE- 47	4.18	0	Hydrophobic	false
C77	CD1	ILE- 47	4.19	0	Hydrophobic	false
O1	N	ILE- 50	3.28	143.18	H-Bond (Protein Donor)	false
O1	N	ILE- 50	3.28	154.69	H-Bond (Protein Donor)	false
C33	CG1	ILE- 50	4.38	0	Hydrophobic	false
C67	CG1	ILE- 50	3.99	0	Hydrophobic	false
C21	CD1	ILE- 50	3.38	0	Hydrophobic	false
C79	CD1	ILE- 50	3.74	0	Hydrophobic	false
C34	CG	PRO- 81	3.82	0	Hydrophobic	false
C66	CG	PRO- 81	4.02	0	Hydrophobic	false
C35	CG1	VAL- 82	3.43	0	Hydrophobic	false
C65	CG1	VAL- 82	3.76	0	Hydrophobic	false
C22	CG1	VAL- 84	3.81	0	Hydrophobic	false
C31	CG2	VAL- 84	4.41	0	Hydrophobic	false
C78	CG1	VAL- 84	3.83	0	Hydrophobic	false