scPDB - 2e41 entry

Protein Data Bank Entry:

PDB ID : 2e41

Resolution :1.750 Å

Experimental Method : X-ray

Deposition Date : 2006-12-01

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	235aa long hypothetical biotin--[acetyl-CoA-carboxylase] ligase
ID:	O57883_PYRHO
AC:	O57883
Organism:	Pyrococcus horikoshii
Reign:	Archaea
TaxID:	70601
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	16.268
Number of residues:	46
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.206	455.625

% Hydrophobic	% Polar
48.15	51.85
According to VolSite

Ligand :

HET Code:	BTX
Formula:	C20H29N7O8PS
Molecular weight:	558.525 g/mol
DrugBank ID:	DB04651
Buried Surface Area:	69.94 %
Polar Surface area:	254.13 Å2

Number of
H-Bond Acceptors:	13
H-Bond Donors:	5
Rings:	5
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
-19.5266	-8.6773	-4.71162

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
O3B	OG	SER- 21	2.61	137.26	H-Bond (Protein Donor)	false
N1B	OE1	GLN- 42	2.81	121.2	H-Bond (Ligand Donor)	false
O3B	N	HIS- 46	2.96	161.76	H-Bond (Protein Donor)	false
N2B	O	HIS- 46	2.85	167.07	H-Bond (Ligand Donor)	false
O2P	N	ALA- 48	2.88	157.85	H-Bond (Protein Donor)	false
O2P	NH2	ARG- 51	2.68	134.16	H-Bond (Protein Donor)	false
O2P	NE	ARG- 51	3.25	121.44	H-Bond (Protein Donor)	false
O2P	CZ	ARG- 51	3.32	0	Ionic (Protein Cationic)	false
C5'	CB	ARG- 51	4.29	0	Hydrophobic	false
C3'	CG	ARG- 51	4.33	0	Hydrophobic	false
C1'	CZ3	TRP- 53	4.28	0	Hydrophobic	false
CBB	CZ3	TRP- 53	3.77	0	Hydrophobic	false
C5'	CE3	TRP- 53	3.92	0	Hydrophobic	false
C7B	CD2	TRP- 53	3.82	0	Hydrophobic	false
DuAr	DuAr	TRP- 53	3.71	0	Aromatic Face/Face	false
N7	N	GLU- 54	2.89	145.33	H-Bond (Protein Donor)	false
N6	O	GLU- 54	2.93	143.53	H-Bond (Ligand Donor)	false
S1B	CB	TRP- 61	4.19	0	Hydrophobic	false
C8B	CB	LEU- 116	3.76	0	Hydrophobic	false
N6	OD1	ASN- 131	3.13	166.25	H-Bond (Ligand Donor)	false
N1	ND2	ASN- 131	2.86	175.91	H-Bond (Protein Donor)	false