scPDB - 3c41 entry

Protein Data Bank Entry:

PDB ID : 3c41

Resolution :2.250 Å

Experimental Method : X-ray

Deposition Date : 2008-01-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Amino acid ABC transporter
ID:	D0VWX4_GEOSE
AC:	D0VWX4
Organism:	Geobacillus stearothermophilus
Reign:	Bacteria
TaxID:	1422
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
J	81 %
K	19 %

Ligand binding site composition:

B-Factor:	39.819
Number of residues:	28
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.022	550.125

% Hydrophobic	% Polar
43.56	56.44
According to VolSite

Ligand :

HET Code:	ANP
Formula:	C10H13N6O12P3
Molecular weight:	502.164 g/mol
DrugBank ID:	-
Buried Surface Area:	51 %
Polar Surface area:	322.68 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
19.6235	4.67048	3.03884

Binding mode :

What is Poseview ?

2D View
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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
C1'	CD2	PHE- 11	4.31	0	Hydrophobic	false
DuAr	DuAr	PHE- 11	3.35	0	Aromatic Face/Face	false
C5'	CG1	VAL- 16	3.38	0	Hydrophobic	false
C1'	CG2	VAL- 16	3.72	0	Hydrophobic	false
C4'	CG2	VAL- 16	3.21	0	Hydrophobic	false
O1G	OG	SER- 36	2.78	162.03	H-Bond (Protein Donor)	false
O1B	N	GLY- 37	3.44	130.79	H-Bond (Protein Donor)	false
O1B	N	SER- 38	3.48	122.1	H-Bond (Protein Donor)	false
O3A	N	GLY- 39	3.39	142.58	H-Bond (Protein Donor)	false
O2G	NZ	LYS- 40	2.66	137.97	H-Bond (Protein Donor)	false
O1B	N	LYS- 40	3.33	150.76	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 40	2.68	143.51	H-Bond (Protein Donor)	false
O2G	NZ	LYS- 40	2.66	0	Ionic (Protein Cationic)	false
O1B	NZ	LYS- 40	2.68	0	Ionic (Protein Cationic)	false
O2B	N	SER- 41	3.09	151.35	H-Bond (Protein Donor)	false
O1A	N	THR- 42	2.86	155.75	H-Bond (Protein Donor)	false
O1A	OG1	THR- 42	2.87	159.71	H-Bond (Protein Donor)	false
O3G	MG	MG- 603	2.15	0	Metal Acceptor	false
O2B	MG	MG- 603	2.35	0	Metal Acceptor	false