scPDB - 4s1h entry

Protein Data Bank Entry:

PDB ID : 4s1h

Resolution :1.600 Å

Experimental Method : X-ray

Deposition Date : 2015-01-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Pyridoxal kinase, putative
ID:	C4LVZ4_ENTHI
AC:	C4LVZ4
Organism:	Entamoeba histolytica
Reign:	Eukaryota
TaxID:	5759
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	26.048
Number of residues:	42
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	2
Water Molecules:	2
Cofactors:
Metals:	MG MG

Cavity properties

Ligandability	Volume (Å3)
0.953	681.750

% Hydrophobic	% Polar
51.98	48.02
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	75.72 %
Polar Surface area:	260.7 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
-13.3179	20.7258	31.5763

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
O1B	ND2	ASN- 143	2.99	168.91	H-Bond (Protein Donor)	false
O2A	OG1	THR- 179	2.67	175.96	H-Bond (Protein Donor)	false
C5'	CB	THR- 179	4.21	0	Hydrophobic	false
O3'	O	THR- 179	2.62	171.09	H-Bond (Ligand Donor)	false
O2A	OG	SER- 180	2.63	153.07	H-Bond (Protein Donor)	false
C2'	CD1	ILE- 206	4.2	0	Hydrophobic	false
N6	O	ILE- 209	2.77	157.06	H-Bond (Ligand Donor)	false
N1	N	ILE- 209	2.87	169.21	H-Bond (Protein Donor)	false
C5'	CB	VAL- 216	4.26	0	Hydrophobic	false
O2B	N	GLY- 217	2.95	144.29	H-Bond (Protein Donor)	false
C5'	CD2	LEU- 220	4.06	0	Hydrophobic	false
C1'	CD2	LEU- 245	3.84	0	Hydrophobic	false
C4'	CD2	LEU- 245	3.5	0	Hydrophobic	false
O2'	OE1	GLN- 246	3.27	171.75	H-Bond (Ligand Donor)	false
N3	NE2	GLN- 246	3.16	157.72	H-Bond (Protein Donor)	false
C1'	CD1	LEU- 249	4.28	0	Hydrophobic	false
O1B	MG	MG- 303	1.95	0	Metal Acceptor	false
O1A	MG	MG- 303	1.92	0	Metal Acceptor	false
N7	O	HOH- 445	2.82	179.96	H-Bond (Protein Donor)	false