scPDB - 2cem entry

Protein Data Bank Entry:

PDB ID : 2cem

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2006-02-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Pol protein
ID:	Q8Q3H0_9HIV1
AC:	Q8Q3H0
Organism:	Human immunodeficiency virus 1
Reign:	Viruses
TaxID:	11676
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	50 %
B	50 %

Ligand binding site composition:

B-Factor:	9.532
Number of residues:	48
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.045	880.875

% Hydrophobic	% Polar
44.06	55.94
According to VolSite

Ligand :

HET Code:	2AH
Formula:	C39H45N5O6
Molecular weight:	679.804 g/mol
DrugBank ID:	-
Buried Surface Area:	67.47 %
Polar Surface area:	153.12 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	5
Rings:	5
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	14

Mass center Coordinates

X	Y	Z
11.5491	22.7672	5.12958

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
C29	CD2	LEU- 23	3.58	0	Hydrophobic	false
O36	OD2	ASP- 25	2.73	166.42	H-Bond (Ligand Donor)	false
N43	O	GLY- 27	2.99	136.05	H-Bond (Ligand Donor)	false
C50	CB	ALA- 28	3.73	0	Hydrophobic	false
O55	N	ASP- 29	2.93	161.6	H-Bond (Protein Donor)	false
C91	CB	ASP- 29	4.29	0	Hydrophobic	false
C49	CB	ASP- 30	4.32	0	Hydrophobic	false
C50	CG1	VAL- 32	4.31	0	Hydrophobic	false
C92	CD1	ILE- 47	4.01	0	Hydrophobic	false
N51	O	GLY- 48	3.06	166.26	H-Bond (Ligand Donor)	false
C82	CG1	ILE- 50	4.33	0	Hydrophobic	false
C7	CD1	ILE- 50	3.5	0	Hydrophobic	false
C27	CG	PRO- 81	3.71	0	Hydrophobic	false
C28	CG2	VAL- 82	3.68	0	Hydrophobic	false
C29	CB	VAL- 82	4.09	0	Hydrophobic	false
C50	CD1	ILE- 84	3.82	0	Hydrophobic	false
C25	CD1	ILE- 84	3.54	0	Hydrophobic	false
C30	CD1	ILE- 84	3.61	0	Hydrophobic	false
C44	CD2	LEU- 123	4.44	0	Hydrophobic	false
C79	CD2	LEU- 123	4.11	0	Hydrophobic	false
N4	O	GLY- 127	3.37	172.12	H-Bond (Ligand Donor)	false
O14	O	GLY- 127	2.92	144.1	H-Bond (Ligand Donor)	false
C7	CB	ALA- 128	3.54	0	Hydrophobic	false
C12	CB	ASP- 129	4.34	0	Hydrophobic	false
O14	N	ASP- 129	2.89	150.38	H-Bond (Protein Donor)	false
C10	CB	ASP- 130	3.59	0	Hydrophobic	false
C9	CG2	VAL- 132	3.37	0	Hydrophobic	false
C10	CG2	ILE- 147	4.06	0	Hydrophobic	false
C11	CB	ILE- 147	4.47	0	Hydrophobic	false
C9	CD1	ILE- 147	3.94	0	Hydrophobic	false
C27	CD1	ILE- 150	4.37	0	Hydrophobic	false
C26	CG1	ILE- 150	3.79	0	Hydrophobic	false
C92	CG1	ILE- 150	3.44	0	Hydrophobic	false
C81	CB	PRO- 181	4.03	0	Hydrophobic	false
C83	CG	PRO- 181	4.03	0	Hydrophobic	false
C95	CB	PRO- 181	3.28	0	Hydrophobic	false
C80	CG2	VAL- 182	3.77	0	Hydrophobic	false
C7	CD1	ILE- 184	4.19	0	Hydrophobic	false
C44	CD1	ILE- 184	3.63	0	Hydrophobic	false