scPDB - 1gvh entry

Protein Data Bank Entry:

PDB ID : 1gvh

Resolution :2.190 Å

Experimental Method : X-ray

Deposition Date : 2002-02-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Flavohemoprotein
ID:	HMP_ECOLI
AC:	P24232
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	18.789
Number of residues:	48
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.939	1674.000

% Hydrophobic	% Polar
56.45	43.55
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	59.08 %
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
59.6727	25.8364	109.403

Binding mode :

What is Poseview ?

2D View
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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
O1A	ND2	ASN- 44	2.95	160.46	H-Bond (Protein Donor)	false
C2B	CG	GLN- 48	4.02	0	Hydrophobic	false
C3B	CG	GLN- 48	4.09	0	Hydrophobic	false
C6	CB	TYR- 188	4.37	0	Hydrophobic	false
C7M	CD2	TYR- 188	3.33	0	Hydrophobic	false
O1A	CZ	ARG- 204	3.94	0	Ionic (Protein Cationic)	false
C5'	CD	ARG- 204	4.11	0	Hydrophobic	false
O2'	O	GLN- 205	2.67	156.8	H-Bond (Ligand Donor)	false
O2'	N	GLN- 205	3.44	129.77	H-Bond (Protein Donor)	false
C7	CB	GLN- 205	3.87	0	Hydrophobic	false
C8	CB	GLN- 205	3.88	0	Hydrophobic	false
C2'	CE1	TYR- 206	3.86	0	Hydrophobic	false
C4'	CZ	TYR- 206	4.37	0	Hydrophobic	false
O4	OG	SER- 207	3.45	124.75	H-Bond (Protein Donor)	false
O4	N	SER- 207	3.06	143.24	H-Bond (Protein Donor)	false
N5	OG	SER- 207	2.96	163.78	H-Bond (Protein Donor)	false
N5	N	SER- 207	3.16	140.61	H-Bond (Protein Donor)	false
N3	O	ALA- 220	2.9	154.73	H-Bond (Ligand Donor)	false
O2	N	LYS- 222	2.89	159.44	H-Bond (Protein Donor)	false
C1B	CB	GLU- 224	4.41	0	Hydrophobic	false
C4B	CB	GLU- 224	4.03	0	Hydrophobic	false
O3B	O	GLU- 225	2.87	123.93	H-Bond (Ligand Donor)	false
O2A	N	GLN- 228	3.25	171.81	H-Bond (Protein Donor)	false
O3P	N	GLN- 228	3.32	122.91	H-Bond (Protein Donor)	false
O1P	N	SER- 230	2.84	138.31	H-Bond (Protein Donor)	false
O2P	N	SER- 230	3.43	159.61	H-Bond (Protein Donor)	false
O2P	OG	SER- 230	2.8	167.28	H-Bond (Protein Donor)	false
C7M	CG	GLU- 388	4.43	0	Hydrophobic	false
C1'	CB	PHE- 390	4.02	0	Hydrophobic	false
C9A	CG	PHE- 390	3.47	0	Hydrophobic	false
O4	O	HOH- 2095	2.76	174.18	H-Bond (Protein Donor)	false