scPDB - 4dbv entry

Protein Data Bank Entry:

PDB ID : 4dbv

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 1997-01-06

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:	G3P_GEOSE
AC:	P00362
Organism:	Geobacillus stearothermophilus
Reign:	Bacteria
TaxID:	1422
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
P	91 %
Q	9 %

Ligand binding site composition:

B-Factor:	22.763
Number of residues:	50
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.549	668.250

% Hydrophobic	% Polar
37.37	62.63
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	53.49 %
Polar Surface area:	404.9 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	5
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
35.7062	21.5231	28.5442

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- 10	3.07	169.32	H-Bond (Protein Donor)	false
O2N	N	ILE- 11	2.87	169.82	H-Bond (Protein Donor)	false
C3N	CG1	ILE- 11	3.5	0	Hydrophobic	false
C4N	CD1	ILE- 11	3.64	0	Hydrophobic	false
O3B	OD1	ASP- 32	2.89	165.24	H-Bond (Ligand Donor)	false
O3X	OG1	THR- 33	3.24	155.81	H-Bond (Protein Donor)	false
N6A	O	ARG- 77	2.99	171.34	H-Bond (Ligand Donor)	false
C1B	CG2	THR- 96	4.49	0	Hydrophobic	false
O4D	OG	SER- 119	3.46	162.17	H-Bond (Protein Donor)	false
C2D	CB	ALA- 120	4.46	0	Hydrophobic	false
C4N	SG	CYS- 149	3.72	0	Hydrophobic	false
C5N	CB	CYS- 149	3.95	0	Hydrophobic	false
O2A	ND2	ASN- 180	3.17	132.64	H-Bond (Protein Donor)	false
O7N	ND2	ASN- 313	3.11	174.47	H-Bond (Protein Donor)	false
C5N	CB	TYR- 317	4.34	0	Hydrophobic	false
C5N	CD2	TYR- 317	3.33	0	Hydrophobic	false
O2A	O	HOH- 341	2.92	179.98	H-Bond (Protein Donor)	false
O2N	O	HOH- 355	2.9	179.97	H-Bond (Protein Donor)	false