scPDB - 1k2c entry

Protein Data Bank Entry:

PDB ID : 1k2c

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2001-09-26

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_HV1B5
AC:	P04587
Organism:	Human immunodeficiency virus type 1 group M subtype B
Reign:	Viruses
TaxID:	11682
EC Number:	3.4.23.16

Chains:

Chain Name:	Percentage of Residues within binding site
A	44 %
B	56 %

Ligand binding site composition:

B-Factor:	16.142
Number of residues:	43
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.951	637.875

% Hydrophobic	% Polar
43.39	56.61
According to VolSite

Ligand :

HET Code:	0Q4
Formula:	C40H71N11O8
Molecular weight:	834.061 g/mol
DrugBank ID:	-
Buried Surface Area:	55.4 %
Polar Surface area:	336.61 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	11
Rings:	1
Aromatic rings:	1
Anionic atoms:	1
Cationic atoms:	3
Rule of Five Violation:	3
Rotatable Bonds:	30

Mass center Coordinates

X	Y	Z
21.955	30.3533	12.9586

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
CD1	CD2	LEU- 23	3.32	0	Hydrophobic	false
CD11	CD2	LEU- 23	3.66	0	Hydrophobic	false
N2	O	GLY- 27	3.14	143.81	H-Bond (Ligand Donor)	false
N4	O	GLY- 27	3.18	165.82	H-Bond (Ligand Donor)	false
CB4	CB	ALA- 28	3.85	0	Hydrophobic	false
CB1	CB	ALA- 28	3.81	0	Hydrophobic	false
N	OD2	ASP- 29	3.05	161.99	H-Bond (Ligand Donor)	false
N	OD2	ASP- 29	3.05	0	Ionic (Ligand Cationic)	false
O	N	ASP- 29	2.84	166.81	H-Bond (Protein Donor)	false
O3	N	ASP- 29	3	162.57	H-Bond (Protein Donor)	false
CE	CB	ASP- 29	4.23	0	Hydrophobic	false
N	OD1	ASN- 30	2.87	162.7	H-Bond (Ligand Donor)	false
CG1	CB	ASN- 30	4.31	0	Hydrophobic	false
OE1	N	ASN- 30	2.85	158.66	H-Bond (Protein Donor)	false
OE2	ND2	ASN- 30	2.62	155.86	H-Bond (Protein Donor)	false
CG1	CG2	VAL- 32	3.71	0	Hydrophobic	false
CG5	CG2	VAL- 32	4.03	0	Hydrophobic	false
N7	O	MET- 46	2.75	131.74	H-Bond (Ligand Donor)	false
CG2	CD1	ILE- 47	4.31	0	Hydrophobic	false
CG5	CD1	ILE- 47	3.66	0	Hydrophobic	false
N1	O	GLY- 48	3.02	166.07	H-Bond (Ligand Donor)	false
N5	O	GLY- 48	2.93	161.07	H-Bond (Ligand Donor)	false
O4	N	GLY- 48	2.72	169.79	H-Bond (Protein Donor)	false
CG2	CG1	ILE- 50	3.34	0	Hydrophobic	false
CD2	CD1	ILE- 50	4.07	0	Hydrophobic	false
CB3	CD1	ILE- 50	4.47	0	Hydrophobic	false
CB4	CG1	ILE- 50	4.23	0	Hydrophobic	false
CD2	CG	PRO- 81	4	0	Hydrophobic	false
CE2	CG	PRO- 81	3.82	0	Hydrophobic	false
CD1	CB	SER- 82	3.85	0	Hydrophobic	false
CE2	CB	SER- 82	4.5	0	Hydrophobic	false
CD2	CD1	ILE- 84	3.92	0	Hydrophobic	false
CD1	CD1	ILE- 84	3.25	0	Hydrophobic	false
CB3	CD1	ILE- 84	3.83	0	Hydrophobic	false