scPDB - 4xb2 entry

Protein Data Bank Entry:

PDB ID : 4xb2

Resolution :2.430 Å

Experimental Method : X-ray

Deposition Date : 2014-12-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	319aa long hypothetical homoserine dehydrogenase
ID:	O58802_PYRHO
AC:	O58802
Organism:	Pyrococcus horikoshii
Reign:	Archaea
TaxID:	70601
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	32.833
Number of residues:	43
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	1
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.693	725.625

% Hydrophobic	% Polar
37.21	62.79
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	53.95 %
Polar Surface area:	404.9 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	5
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
8.70029	-11.7033	-22.7926

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
O3B	N	PHE- 10	2.83	157.12	H-Bond (Protein Donor)	false
O2A	OG1	THR- 12	3.39	152.51	H-Bond (Protein Donor)	false
O2A	N	THR- 12	2.95	157.58	H-Bond (Protein Donor)	false
O1N	N	VAL- 13	2.84	161.93	H-Bond (Protein Donor)	false
C5D	CG2	VAL- 13	3.96	0	Hydrophobic	false
C3N	CG2	VAL- 13	4.28	0	Hydrophobic	false
O3X	NE	ARG- 40	2.79	141.87	H-Bond (Protein Donor)	false
O3X	CZ	ARG- 40	3.93	0	Ionic (Protein Cationic)	false
C4B	CB	SER- 92	4.48	0	Hydrophobic	false
C1B	CB	SER- 92	4.15	0	Hydrophobic	false
O3D	O	SER- 92	2.75	165.56	H-Bond (Ligand Donor)	false
C5B	CB	SER- 93	4.25	0	Hydrophobic	false
O4B	N	SER- 93	3.22	152.81	H-Bond (Protein Donor)	false
C4D	CB	SER- 114	4.47	0	Hydrophobic	false
O4D	OG	SER- 114	2.75	161.98	H-Bond (Protein Donor)	false
O2D	NZ	LYS- 116	3.37	144.94	H-Bond (Protein Donor)	false
C4N	CB	ALA- 145	4.28	0	Hydrophobic	false
O7N	N	GLY- 296	2.8	162.6	H-Bond (Protein Donor)	false
C4N	CG2	THR- 300	3.79	0	Hydrophobic	false
C4N	C4	HSE- 1002	3.76	0	Hydrophobic	false
O1N	O	HOH- 1167	2.71	174.89	H-Bond (Protein Donor)	false
O2D	O	HOH- 1176	2.86	179.95	H-Bond (Protein Donor)	false