scPDB - 2d2i entry

Protein Data Bank Entry:

PDB ID : 2d2i

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2005-09-09

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glyceraldehyde-3-phosphate dehydrogenase
ID:	Q55245_SYNSP
AC:	Q55245
Organism:	Synechococcus sp
Reign:	Bacteria
TaxID:	1131
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	21.361
Number of residues:	44
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.966	496.125

% Hydrophobic	% Polar
47.62	52.38
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	56.14 %
Polar Surface area:	405.54 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	5
Rings:	5
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
18.0671	62.1718	10.7168

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
O2A	N	ARG- 12	2.86	165.48	H-Bond (Protein Donor)	false
O2N	N	ILE- 13	3.02	171.13	H-Bond (Protein Donor)	false
C5D	CG1	ILE- 13	4.12	0	Hydrophobic	false
C3N	CD1	ILE- 13	3.48	0	Hydrophobic	false
O3B	OD1	ASN- 36	3.29	139.4	H-Bond (Ligand Donor)	false
C1B	CG2	THR- 37	3.94	0	Hydrophobic	false
N7A	NH1	ARG- 80	3.13	132.31	H-Bond (Protein Donor)	false
N6A	O	ARG- 80	3.25	167.04	H-Bond (Ligand Donor)	false
C1B	CB	THR- 99	4.49	0	Hydrophobic	false
C3D	CB	ALA- 123	4.27	0	Hydrophobic	false
C4N	SG	CYS- 155	3.26	0	Hydrophobic	false
O7N	ND2	ASN- 318	2.75	161.21	H-Bond (Protein Donor)	false
C5N	CD2	TYR- 322	3.35	0	Hydrophobic	false
C5N	CB	TYR- 322	4.42	0	Hydrophobic	false
O2N	O	HOH- 6488	2.77	157.96	H-Bond (Protein Donor)	false