scPDB - 1wkh entry

Protein Data Bank Entry:

PDB ID : 1wkh

Resolution :2.250 Å

Experimental Method : X-ray

Deposition Date : 2004-05-31

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	[LysW]-aminoadipate semialdehyde transaminase
ID:	ARGD_THET8
AC:	Q5SHH5
Organism:	Thermus thermophilus
Reign:	Bacteria
TaxID:	300852
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	82 %
B	18 %

Ligand binding site composition:

B-Factor:	13.439
Number of residues:	41
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.937	1029.375

% Hydrophobic	% Polar
45.25	54.75
According to VolSite

Ligand :

HET Code:	PPE
Formula:	C13H16N2O9P
Molecular weight:	375.248 g/mol
DrugBank ID:	DB01813
Buried Surface Area:	68.51 %
Polar Surface area:	212.22 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	2
Rings:	1
Aromatic rings:	1
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
33.6956	2.4062	60.1702

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
CBA	CD2	TYR- 54	3.75	0	Hydrophobic	false
OP1	N	GLY- 113	2.86	165.82	H-Bond (Protein Donor)	false
C5A	CB	THR- 114	4.47	0	Hydrophobic	false
OP3	N	THR- 114	2.99	165.22	H-Bond (Protein Donor)	false
C5A	CE2	PHE- 140	3.85	0	Hydrophobic	false
CGA	CE2	PHE- 140	3.95	0	Hydrophobic	false
C4	CD2	PHE- 140	3.49	0	Hydrophobic	false
C2A	CG	GLU- 192	3.78	0	Hydrophobic	false
N1	OD1	ASP- 225	3.39	128.23	H-Bond (Ligand Donor)	false
N1	OD2	ASP- 225	2.81	175.31	H-Bond (Ligand Donor)	false
C2A	CB	ILE- 227	4.48	0	Hydrophobic	false
C5	CG2	ILE- 227	4.2	0	Hydrophobic	false
C2A	CB	GLN- 228	4.31	0	Hydrophobic	false
OP2	OG1	THR- 283	2.78	161.12	H-Bond (Protein Donor)	false
OP2	N	THR- 283	3.09	147.65	H-Bond (Protein Donor)	false
OA	NH1	ARG- 371	3.1	172.96	H-Bond (Protein Donor)	false
OA	CZ	ARG- 371	3.86	0	Ionic (Protein Cationic)	false
OXT	CZ	ARG- 371	3.5	0	Ionic (Protein Cationic)	false