scPDB - 3c3c entry

Protein Data Bank Entry:

PDB ID : 3c3c

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2008-01-28

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Phosphoglycerate kinase 1
ID:	PGK1_HUMAN
AC:	P00558
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.7.2.3

Chains:

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

Ligand binding site composition:

B-Factor:	27.826
Number of residues:	28
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.770	290.250

% Hydrophobic	% Polar
68.60	31.40
According to VolSite

Ligand :

HET Code:	CDP
Formula:	C9H12N3O11P2
Molecular weight:	400.153 g/mol
DrugBank ID:	DB04555
Buried Surface Area:	50.69 %
Polar Surface area:	249.77 Å2

Number of
H-Bond Acceptors:	13
H-Bond Donors:	3
Rings:	2
Aromatic rings:	0
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
12.1752	-0.9662	34.5753

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
O1A	N	ALA- 214	2.93	148.53	H-Bond (Protein Donor)	false
O5'	N	ALA- 214	3.13	138.75	H-Bond (Protein Donor)	false
C5'	CB	ALA- 214	4.35	0	Hydrophobic	false
O2B	NZ	LYS- 219	3.77	0	Ionic (Protein Cationic)	false
O1A	NZ	LYS- 219	2.76	0	Ionic (Protein Cationic)	false
O1A	NZ	LYS- 219	2.76	129.17	H-Bond (Protein Donor)	false
O2	N	GLY- 238	3.21	127.11	H-Bond (Protein Donor)	false
C1'	CG	PRO- 338	3.76	0	Hydrophobic	false
O3'	OE2	GLU- 343	2.73	166.34	H-Bond (Ligand Donor)	false
O2'	OE1	GLU- 343	2.89	159.97	H-Bond (Ligand Donor)	false