scPDB - 2xej entry

Protein Data Bank Entry:

PDB ID : 2xej

Resolution :1.780 Å

Experimental Method : X-ray

Deposition Date : 2010-05-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glutamate carboxypeptidase 2
ID:	FOLH1_HUMAN
AC:	Q04609
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.4.17.21

Chains:

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

Ligand binding site composition:

B-Factor:	19.593
Number of residues:	53
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	3
Water Molecules:	4
Cofactors:
Metals:	CL ZN ZN

Cavity properties

Ligandability	Volume (Å3)
0.729	1110.375

% Hydrophobic	% Polar
34.65	65.35
According to VolSite

Ligand :

HET Code:	OKD
Formula:	C24H38N5O12
Molecular weight:	588.585 g/mol
DrugBank ID:	-
Buried Surface Area:	45.77 %
Polar Surface area:	238.37 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	2
Rings:	1
Aromatic rings:	1
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	26

Mass center Coordinates

X	Y	Z
22.4312	49.708	41.2889

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	CE1	PHE- 209	4.44	0	Hydrophobic	false
OAH	NH1	ARG- 210	2.73	160.44	H-Bond (Protein Donor)	false
OAH	NH2	ARG- 210	3.34	129.28	H-Bond (Protein Donor)	false
OAH	CZ	ARG- 210	3.46	0	Ionic (Protein Cationic)	false
OAB	ND2	ASN- 257	2.93	170.21	H-Bond (Protein Donor)	false
NBB	OE2	GLU- 424	3.04	126.76	H-Bond (Ligand Donor)	false
CAT	CD2	LEU- 428	3.91	0	Hydrophobic	false
N	O	GLY- 518	3.05	150.48	H-Bond (Ligand Donor)	false
NBB	O	GLY- 518	3.05	134.92	H-Bond (Ligand Donor)	false
O	ND2	ASN- 519	2.91	158.3	H-Bond (Protein Donor)	false
O	NH2	ARG- 534	2.86	166.96	H-Bond (Protein Donor)	false
O	CZ	ARG- 534	3.84	0	Ionic (Protein Cationic)	false
OXT	NH2	ARG- 536	2.93	148.22	H-Bond (Protein Donor)	false
OXT	NH1	ARG- 536	2.98	145.42	H-Bond (Protein Donor)	false
OXT	CZ	ARG- 536	3.4	0	Ionic (Protein Cationic)	false
CAK	CZ	TYR- 552	3.9	0	Hydrophobic	false
CAJ	CE1	TYR- 552	3.84	0	Hydrophobic	false
CB	CZ	TYR- 552	4.07	0	Hydrophobic	false
OAE	OH	TYR- 552	2.59	172.65	H-Bond (Protein Donor)	false
OBG	ND2	ASN- 698	3.31	168.88	H-Bond (Protein Donor)	false
OAF	NZ	LYS- 699	2.62	154.77	H-Bond (Protein Donor)	false
OAF	NZ	LYS- 699	2.62	0	Ionic (Protein Cationic)	false
OAB	NZ	LYS- 699	3.79	0	Ionic (Protein Cationic)	false
CAX	CD2	TYR- 700	4.12	0	Hydrophobic	false
CAK	CZ	TYR- 700	3.78	0	Hydrophobic	false
CB	CE1	TYR- 700	3.78	0	Hydrophobic	false
CAS	CB	TYR- 700	4.08	0	Hydrophobic	false
OAD	OH	TYR- 700	2.52	165.48	H-Bond (Protein Donor)	false
CAR	CB	ALA- 701	3.88	0	Hydrophobic	false
CAQ	CB	ALA- 701	3.66	0	Hydrophobic	false
OAE	ZN	ZN- 1751	2.61	0	Metal Acceptor	false
OAH	O	HOH- 2561	2.65	179.94	H-Bond (Protein Donor)	false
O	O	HOH- 2562	2.69	160.79	H-Bond (Protein Donor)	false