scPDB - 1c9k entry

Protein Data Bank Entry:

PDB ID : 1c9k

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 1999-08-02

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Bifunctional adenosylcobalamin biosynthesis protein CobU
ID:	COBU_SALTY
AC:	Q05599
Organism:	Salmonella typhimurium
Reign:	Bacteria
TaxID:	99287
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	5 %
B	95 %

Ligand binding site composition:

B-Factor:	44.671
Number of residues:	23
Including
Standard Amino Acids:	22
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.081	1242.000

% Hydrophobic	% Polar
34.51	65.49
According to VolSite

Ligand :

HET Code:	5GP
Formula:	C10H12N5O8P
Molecular weight:	361.205 g/mol
DrugBank ID:	-
Buried Surface Area:	57.02 %
Polar Surface area:	217.22 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
7.31352	36.0357	19.0232

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
C2'	CB	ALA- 30	4.44	0	Hydrophobic	false
O3'	OG	SER- 32	3.44	126.75	H-Bond (Ligand Donor)	false
O2'	OG	SER- 32	2.52	169.82	H-Bond (Ligand Donor)	false
N2	O	SER- 32	2.99	141.55	H-Bond (Ligand Donor)	false
O2'	N	SER- 32	3.38	144.05	H-Bond (Protein Donor)	false
C1'	CB	SER- 32	4.27	0	Hydrophobic	false
C1'	CG1	ILE- 43	4.11	0	Hydrophobic	false
N7	NH2	ARG- 50	2.63	143.47	H-Bond (Protein Donor)	false
O6	NH1	ARG- 50	2.92	173.38	H-Bond (Protein Donor)	false
N2	OE1	GLU- 58	3.27	158.7	H-Bond (Ligand Donor)	false
C3'	CG	GLU- 80	3.72	0	Hydrophobic	false
C2'	CB	GLU- 80	4	0	Hydrophobic	false