scPDB - 5kwv entry

Protein Data Bank Entry:

PDB ID : 5kwv

Resolution :2.250 Å

Experimental Method : X-ray

Deposition Date : 2016-07-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Pantothenate synthetase
ID:	B4RKE7_NEIG2
AC:	B4RKE7
Organism:	Neisseria gonorrhoeae
Reign:	Bacteria
TaxID:	521006
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	71.207
Number of residues:	35
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.801	945.000

% Hydrophobic	% Polar
37.50	62.50
According to VolSite

Ligand :

HET Code:	ANP
Formula:	C10H13N6O12P3
Molecular weight:	502.164 g/mol
DrugBank ID:	-
Buried Surface Area:	65.53 %
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
10.9778	92.4639	18.1473

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
O2B	NE2	HIS- 30	3.09	151.1	H-Bond (Protein Donor)	false
O3A	NE2	HIS- 33	2.95	141.64	H-Bond (Protein Donor)	false
C2'	CD1	LEU- 36	4.07	0	Hydrophobic	false
O1G	NZ	LYS- 146	3.15	169.29	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 146	3.15	0	Ionic (Protein Cationic)	false
O1B	NZ	LYS- 146	3.93	0	Ionic (Protein Cationic)	false
O3'	OE1	GLN- 150	3.26	154.37	H-Bond (Ligand Donor)	false
N6	O	GLY- 173	3.1	145.52	H-Bond (Ligand Donor)	false
N1	N	GLY- 173	3.02	151.36	H-Bond (Protein Donor)	false
N6	O	LEU- 181	2.75	156.55	H-Bond (Ligand Donor)	false
O1G	OG	SER- 182	2.66	142.85	H-Bond (Protein Donor)	false
O3G	CZ	ARG- 184	3.51	0	Ionic (Protein Cationic)	false