scPDB - 2wqp entry

Protein Data Bank Entry:

PDB ID : 2wqp

Resolution :1.750 Å

Experimental Method : X-ray

Deposition Date : 2009-08-25

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Polysialic acid capsule biosynthesis protein SiaC
ID:	Q7DDU0_NEIMB
AC:	Q7DDU0
Organism:	Neisseria meningitidis serogroup B
Reign:	Bacteria
TaxID:	122586
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	8.414
Number of residues:	43
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	MN

Cavity properties

Ligandability	Volume (Å3)
0.448	546.750

% Hydrophobic	% Polar
41.36	58.64
According to VolSite

Ligand :

HET Code:	WQP
Formula:	C11H19NO12P
Molecular weight:	388.242 g/mol
DrugBank ID:	-
Buried Surface Area:	74.28 %
Polar Surface area:	252.61 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	6
Rings:	0
Aromatic rings:	0
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
96.2359	-22.5472	51.6333

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
CAT	CD1	ILE- 28	4.15	0	Hydrophobic	false
OAV	NZ	LYS- 53	3.23	0	Ionic (Protein Cationic)	false
OAL	NZ	LYS- 53	3.31	0	Ionic (Protein Cationic)	false
OAX	NE2	GLN- 55	2.97	167.39	H-Bond (Protein Donor)	false
OAJ	OE1	GLN- 55	3.41	142.43	H-Bond (Ligand Donor)	false
OAY	ND2	ASN- 74	3.08	158.75	H-Bond (Protein Donor)	false
OAK	OD1	ASN- 74	3.17	151.67	H-Bond (Ligand Donor)	false
CAU	CD1	ILE- 79	4.07	0	Hydrophobic	false
CAS	CE	MET- 83	4.41	0	Hydrophobic	false
CAU	CE	MET- 83	4.02	0	Hydrophobic	false
OAV	OG1	THR- 110	2.64	161.3	H-Bond (Protein Donor)	false
OAA	NZ	LYS- 129	2.83	159.31	H-Bond (Protein Donor)	false
OAV	NZ	LYS- 129	2.89	166.85	H-Bond (Protein Donor)	false
OAA	NZ	LYS- 129	2.83	0	Ionic (Protein Cationic)	false
OAV	NZ	LYS- 129	2.89	0	Ionic (Protein Cationic)	false
OAE	OG	SER- 132	2.75	156.4	H-Bond (Protein Donor)	false
OAE	N	SER- 132	3.02	158.08	H-Bond (Protein Donor)	false
OAA	OG	SER- 154	2.51	142.37	H-Bond (Protein Donor)	false
CAG	CE	MET- 157	4.38	0	Hydrophobic	false
OAE	ND2	ASN- 184	3.09	158.25	H-Bond (Protein Donor)	false
OAW	OH	TYR- 186	2.67	155.37	H-Bond (Protein Donor)	false
NAI	OH	TYR- 186	2.89	154.74	H-Bond (Ligand Donor)	false
CAR	CZ	TYR- 186	4.07	0	Hydrophobic	false
OAA	OG	SER- 213	2.58	169.08	H-Bond (Protein Donor)	false
OAX	OD2	ASP- 247	2.62	146.25	H-Bond (Ligand Donor)	false
OAY	OD1	ASP- 247	2.62	144.98	H-Bond (Ligand Donor)	false
OAC	MN	MN- 1351	2.19	0	Metal Acceptor	false
OAW	MN	MN- 1351	2.61	0	Metal Acceptor	false
OAB	O	HOH- 2141	2.96	136.99	H-Bond (Protein Donor)	false