scPDB - 1qwj entry

Protein Data Bank Entry:

PDB ID : 1qwj

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2003-09-02

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	N-acylneuraminate cytidylyltransferase
ID:	NEUA_MOUSE
AC:	Q99KK2
Organism:	Mus musculus
Reign:	Eukaryota
TaxID:	10090
EC Number:	2.7.7.43

Chains:

Chain Name:	Percentage of Residues within binding site
C	82 %
D	18 %

Ligand binding site composition:

B-Factor:	55.705
Number of residues:	46
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.878	1518.750

% Hydrophobic	% Polar
30.67	69.33
According to VolSite

Ligand :

HET Code:	NCC
Formula:	C20H29N4O16P
Molecular weight:	612.435 g/mol
DrugBank ID:	DB02485
Buried Surface Area:	62.72 %
Polar Surface area:	336.16 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	8
Rings:	3
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
99.0565	-10.415	53.4924

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
C1'	CB	LEU- 48	4.44	0	Hydrophobic	false
O2'	O	LEU- 48	3.28	164.06	H-Bond (Ligand Donor)	false
N3	NE	ARG- 50	3.31	150.75	H-Bond (Protein Donor)	false
O2	N	ARG- 50	2.85	143.68	H-Bond (Protein Donor)	false
O3'	NZ	LYS- 59	3.24	162.06	H-Bond (Protein Donor)	false
O2'	ND2	ASN- 60	2.81	148.71	H-Bond (Protein Donor)	false
N3	NH2	ARG- 109	3.03	161.25	H-Bond (Protein Donor)	false
O2	NH1	ARG- 109	3.24	164.28	H-Bond (Protein Donor)	false
N4	O	SER- 118	3.13	139.31	H-Bond (Ligand Donor)	false
C18	CB	SER- 120	3.81	0	Hydrophobic	false
C5'	CG	GLN- 141	4.41	0	Hydrophobic	false
C4'	CB	GLN- 141	4.32	0	Hydrophobic	false
O8	NE2	GLN- 141	3.22	149.68	H-Bond (Protein Donor)	false
N5	OE1	GLN- 141	2.65	150.71	H-Bond (Ligand Donor)	false
C3'	CG2	THR- 143	3.91	0	Hydrophobic	false
C13	CE2	PHE- 176	4.47	0	Hydrophobic	false
C15	CD2	PHE- 176	4.24	0	Hydrophobic	false
O7	NH2	ARG- 199	3.07	127.85	H-Bond (Protein Donor)	false
O10	NE	ARG- 199	2.85	169.54	H-Bond (Protein Donor)	false
C20	CD	ARG- 201	4.25	0	Hydrophobic	false
O1A	N	ARG- 202	3.2	132.95	H-Bond (Protein Donor)	false
C15	CB	GLU- 211	4.21	0	Hydrophobic	false
C18	CE1	TYR- 216	3.56	0	Hydrophobic	false
C18	CD1	LEU- 228	3.76	0	Hydrophobic	false