scPDB - 2c6c entry

Protein Data Bank Entry:

PDB ID : 2c6c

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2005-11-09

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:	25.834
Number of residues:	45
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	3
Water Molecules:	6
Cofactors:
Metals:	CL ZN ZN

Cavity properties

Ligandability	Volume (Å3)
0.278	826.875

% Hydrophobic	% Polar
35.92	64.08
According to VolSite

Ligand :

HET Code:	24I
Formula:	C13H13IO6P
Molecular weight:	423.117 g/mol
DrugBank ID:	DB06928
Buried Surface Area:	72.11 %
Polar Surface area:	130.19 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	0
Rings:	1
Aromatic rings:	1
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
17.8147	45.1782	43.5675

Binding mode :

What is Poseview ?

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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
C13	CE1	PHE- 209	4.03	0	Hydrophobic	false
O4	NH2	ARG- 210	3.05	134.44	H-Bond (Protein Donor)	false
O4	NH1	ARG- 210	2.7	155.26	H-Bond (Protein Donor)	false
O4	CZ	ARG- 210	3.29	0	Ionic (Protein Cationic)	false
O6	ND2	ASN- 257	2.96	165.13	H-Bond (Protein Donor)	false
O1	OE2	GLU- 424	2.73	152.72	H-Bond (Protein Donor)	false
C13	CD2	LEU- 428	4.36	0	Hydrophobic	false
C2	CB	SER- 454	4.31	0	Hydrophobic	false
I	CB	SER- 454	3.85	0	Hydrophobic	false
I	CB	GLU- 457	3.75	0	Hydrophobic	false
I	CD	ARG- 536	4.27	0	Hydrophobic	false
I	CE2	TYR- 549	3.77	0	Hydrophobic	false
O2	OH	TYR- 552	2.8	149.67	H-Bond (Protein Donor)	false
O5	NZ	LYS- 699	2.77	153.71	H-Bond (Protein Donor)	false
O5	NZ	LYS- 699	2.77	0	Ionic (Protein Cationic)	false
O6	NZ	LYS- 699	3.73	0	Ionic (Protein Cationic)	false
O2	ZN	ZN- 1751	1.92	0	Metal Acceptor	false
O1	ZN	ZN- 1752	1.91	0	Metal Acceptor	false
O4	O	HOH- 2074	2.82	145.75	H-Bond (Protein Donor)	false