scPDB - 2qcu entry

Protein Data Bank Entry:

PDB ID : 2qcu

Resolution :1.750 Å

Experimental Method : X-ray

Deposition Date : 2007-06-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Aerobic glycerol-3-phosphate dehydrogenase
ID:	GLPD_ECOLI
AC:	P13035
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	1.1.5.3

Chains:

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

Ligand binding site composition:

B-Factor:	21.758
Number of residues:	63
Including
Standard Amino Acids:	63
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.578	560.250

% Hydrophobic	% Polar
49.40	50.60
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	75.09 %
Polar Surface area:	381.7 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	7
Rings:	6
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
22.3208	22.6132	28.0784

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
O4B	N	GLY- 11	3.42	132.07	H-Bond (Protein Donor)	false
C4'	CG2	ILE- 13	3.93	0	Hydrophobic	false
O1P	N	ASN- 14	3.11	152.96	H-Bond (Protein Donor)	false
O2P	ND2	ASN- 14	2.67	152.23	H-Bond (Protein Donor)	false
N3A	N	ALA- 34	3.05	128.16	H-Bond (Protein Donor)	false
C2B	SG	CYS- 39	4.24	0	Hydrophobic	false
C3B	CB	ALA- 40	3.83	0	Hydrophobic	false
O1A	N	THR- 41	3	120.67	H-Bond (Protein Donor)	false
C5'	CB	THR- 41	4.24	0	Hydrophobic	false
C3'	CG2	THR- 41	3.72	0	Hydrophobic	false
C8M	CG2	THR- 41	3.88	0	Hydrophobic	false
O1A	N	SER- 42	3.28	139.2	H-Bond (Protein Donor)	false
O4'	OG	SER- 42	2.89	161.62	H-Bond (Protein Donor)	false
C6	CB	SER- 45	4.15	0	Hydrophobic	false
C9A	CB	SER- 45	3.76	0	Hydrophobic	false
N5	N	SER- 46	2.91	174.55	H-Bond (Protein Donor)	false
N3	O	LEU- 48	2.72	150.06	H-Bond (Ligand Donor)	false
O4	N	LEU- 48	3.29	150.65	H-Bond (Protein Donor)	false
N1A	N	ALA- 172	3	153.18	H-Bond (Protein Donor)	false
C5B	CE3	TRP- 209	4.12	0	Hydrophobic	false
C3B	CZ3	TRP- 209	3.82	0	Hydrophobic	false
C7M	CG2	THR- 270	4.33	0	Hydrophobic	false
C8M	CB	ARG- 317	4.09	0	Hydrophobic	false
C8	CG	ARG- 317	3.5	0	Hydrophobic	false
N1	N	LEU- 355	3.16	148.68	H-Bond (Protein Donor)	false
O2	N	THR- 356	2.66	137.51	H-Bond (Protein Donor)	false
O2	OG1	THR- 356	2.76	142.52	H-Bond (Protein Donor)	false