scPDB - 2y6p entry

Protein Data Bank Entry:

PDB ID : 2y6p

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2011-01-25

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	3-deoxy-manno-octulosonate cytidylyltransferase
ID:	KDSB_AQUAE
AC:	O66914
Organism:	Aquifex aeolicus
Reign:	Bacteria
TaxID:	224324
EC Number:	2.7.7.38

Chains:

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

Ligand binding site composition:

B-Factor:	37.279
Number of residues:	31
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	2
Water Molecules:	0
Cofactors:
Metals:	MG MG

Cavity properties

Ligandability	Volume (Å3)
0.379	1073.250

% Hydrophobic	% Polar
31.13	68.87
According to VolSite

Ligand :

HET Code:	CTP
Formula:	C9H12N3O14P3
Molecular weight:	479.125 g/mol
DrugBank ID:	DB02431
Buried Surface Area:	68.43 %
Polar Surface area:	308.95 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	3
Rings:	2
Aromatic rings:	0
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
63.4983	63.3452	6.43883

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
C1'	CB	PRO- 8	4.38	0	Hydrophobic	false
O3'	O	PRO- 8	2.89	155.76	H-Bond (Ligand Donor)	false
O2'	N	ARG- 10	2.96	139.65	H-Bond (Protein Donor)	false
O1B	NE	ARG- 10	3.48	134.16	H-Bond (Protein Donor)	false
O1B	NH2	ARG- 10	2.95	155.96	H-Bond (Protein Donor)	false
O2B	NE	ARG- 10	3.08	155.39	H-Bond (Protein Donor)	false
O1B	CZ	ARG- 10	3.64	0	Ionic (Protein Cationic)	false
O2B	CZ	ARG- 10	3.91	0	Ionic (Protein Cationic)	false
C2'	CG	ARG- 10	4.08	0	Hydrophobic	false
O2G	OG1	THR- 14	2.73	175.63	H-Bond (Protein Donor)	false
O2G	N	THR- 14	2.68	150.7	H-Bond (Protein Donor)	false
O3G	OG1	THR- 14	3.42	122.97	H-Bond (Protein Donor)	false
O3G	N	THR- 14	3.24	136.53	H-Bond (Protein Donor)	false
O1G	NH2	ARG- 15	2.98	126.82	H-Bond (Protein Donor)	false
O1G	NE	ARG- 15	3.3	121.17	H-Bond (Protein Donor)	false
O3G	NE	ARG- 15	2.88	168.99	H-Bond (Protein Donor)	false
O3G	N	ARG- 15	2.82	161.23	H-Bond (Protein Donor)	false
O1G	CZ	ARG- 15	3.48	0	Ionic (Protein Cationic)	false
O3G	CZ	ARG- 15	3.81	0	Ionic (Protein Cationic)	false
O1A	NZ	LYS- 19	2.94	137.21	H-Bond (Protein Donor)	false
O3A	NZ	LYS- 19	3.14	148.03	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 19	2.94	0	Ionic (Protein Cationic)	false
N4	O	LEU- 70	2.85	163.21	H-Bond (Ligand Donor)	false
N3	NH2	ARG- 76	3	169.84	H-Bond (Protein Donor)	false
O2	NH2	ARG- 76	3.49	124.25	H-Bond (Protein Donor)	false
O2	NE	ARG- 76	2.6	168.95	H-Bond (Protein Donor)	false
O3'	N	GLY- 94	3.31	125.44	H-Bond (Protein Donor)	false
O1A	MG	MG- 1234	2.06	0	Metal Acceptor	false
O2A	MG	MG- 1235	2.04	0	Metal Acceptor	false
O1B	MG	MG- 1235	2.15	0	Metal Acceptor	false
O1G	MG	MG- 1235	2.01	0	Metal Acceptor	false