scPDB - 2xef entry

Protein Data Bank Entry:

PDB ID : 2xef

Resolution :1.590 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:	22.261
Number of residues:	74
Including
Standard Amino Acids:	62
Non Standard Amino Acids:	3
Water Molecules:	9
Cofactors:
Metals:	CL ZN ZN

Cavity properties

Ligandability	Volume (Å3)
0.564	978.750

% Hydrophobic	% Polar
41.38	58.62
According to VolSite

Ligand :

HET Code:	AR8
Formula:	C37H55N8O19
Molecular weight:	915.875 g/mol
DrugBank ID:	-
Buried Surface Area:	57 %
Polar Surface area:	369.74 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	3
Rings:	2
Aromatic rings:	2
Anionic atoms:	5
Cationic atoms:	2
Rule of Five Violation:	2
Rotatable Bonds:	41

Mass center Coordinates

X	Y	Z
24.8162	51.0743	43.8097

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
CBH	CE1	PHE- 209	4.45	0	Hydrophobic	false
OAI	NH1	ARG- 210	2.74	163.42	H-Bond (Protein Donor)	false
OAI	NH2	ARG- 210	3.37	130.45	H-Bond (Protein Donor)	false
OAI	CZ	ARG- 210	3.5	0	Ionic (Protein Cationic)	false
OAG	ND2	ASN- 257	2.81	168.6	H-Bond (Protein Donor)	false
CBH	CD2	LEU- 428	4.09	0	Hydrophobic	false
CAS	CD	ARG- 463	4.43	0	Hydrophobic	false
OAF	OG	SER- 501	3.48	137.58	H-Bond (Protein Donor)	false
CAN	CD	ARG- 511	3.99	0	Hydrophobic	false
CCF	CD	ARG- 511	3.48	0	Hydrophobic	false
DuAr	CZ	ARG- 511	3.97	153.8	Pi/Cation	false
CAT	CB	SER- 513	4.32	0	Hydrophobic	false
CAS	CB	SER- 513	3.88	0	Hydrophobic	false
CAW	CB	LYS- 514	4.39	0	Hydrophobic	false
NBQ	O	GLY- 518	2.98	139.33	H-Bond (Ligand Donor)	false
N	O	GLY- 518	3.06	147.71	H-Bond (Ligand Donor)	false
O	ND2	ASN- 519	2.86	158.55	H-Bond (Protein Donor)	false
O	NH2	ARG- 534	2.89	167.52	H-Bond (Protein Donor)	false
O	CZ	ARG- 534	3.86	0	Ionic (Protein Cationic)	false
OXT	NH2	ARG- 536	2.83	154.29	H-Bond (Protein Donor)	false
OXT	NH1	ARG- 536	3.11	138.74	H-Bond (Protein Donor)	false
OXT	CZ	ARG- 536	3.41	0	Ionic (Protein Cationic)	false
CAL	CB	TRP- 541	4.48	0	Hydrophobic	false
CAN	CB	TRP- 541	3.49	0	Hydrophobic	false
CAR	CH2	TRP- 541	3.5	0	Hydrophobic	false
DuAr	DuAr	TRP- 541	3.94	0	Aromatic Face/Face	false
OAD	OH	TYR- 552	2.69	167.62	H-Bond (Protein Donor)	false
CAQ	CZ	TYR- 552	4.31	0	Hydrophobic	false
CAP	CE1	TYR- 552	3.88	0	Hydrophobic	false
OBY	ND2	ASN- 698	3.36	171.31	H-Bond (Protein Donor)	false
OAA	NZ	LYS- 699	2.64	157.91	H-Bond (Protein Donor)	false
OAA	NZ	LYS- 699	2.64	0	Ionic (Protein Cationic)	false
OAG	NZ	LYS- 699	3.79	0	Ionic (Protein Cationic)	false
OAC	OH	TYR- 700	2.59	161.61	H-Bond (Protein Donor)	false
CB	CE1	TYR- 700	3.87	0	Hydrophobic	false
CAQ	CZ	TYR- 700	3.73	0	Hydrophobic	false
CBK	CE2	TYR- 700	4.36	0	Hydrophobic	false
CBL	CD2	TYR- 700	3.91	0	Hydrophobic	false
CBF	CB	TYR- 700	3.91	0	Hydrophobic	false
CBD	CB	ALA- 701	4.36	0	Hydrophobic	false
CAX	CB	ALA- 701	4.05	0	Hydrophobic	false
OBT	N	GLY- 702	2.64	147.26	H-Bond (Protein Donor)	false
OAD	ZN	ZN- 1751	2.61	0	Metal Acceptor	false
O	O	HOH- 2361	2.8	122.95	H-Bond (Protein Donor)	false
OAI	O	HOH- 2579	2.64	147.21	H-Bond (Protein Donor)	false
OAF	O	HOH- 2581	2.7	179.97	H-Bond (Protein Donor)	false