scPDB - 1u8v entry

Protein Data Bank Entry:

PDB ID : 1u8v

Resolution :1.600 Å

Experimental Method : X-ray

Deposition Date : 2004-08-07

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase
ID:	HDVD_CLOAM
AC:	P55792
Organism:	Clostridium aminobutyricum
Reign:	Bacteria
TaxID:	33953
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	65 %
B	35 %

Ligand binding site composition:

B-Factor:	20.666
Number of residues:	56
Including
Standard Amino Acids:	52
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.920	985.500

% Hydrophobic	% Polar
39.04	60.96
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	61.01 %
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
79.9168	28.3347	30.8067

Binding mode :

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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
O2	N	MET- 149	3.18	156.25	H-Bond (Protein Donor)	false
N1	OG1	THR- 150	2.84	141.18	H-Bond (Protein Donor)	false
O2	N	THR- 150	2.99	159.32	H-Bond (Protein Donor)	false
O2	OG1	THR- 150	3.06	151.9	H-Bond (Protein Donor)	false
C1'	CB	THR- 150	4.05	0	Hydrophobic	false
C3'	CG2	THR- 150	4.1	0	Hydrophobic	false
O2'	OG1	THR- 150	3.15	166	H-Bond (Ligand Donor)	false
O1A	NZ	LYS- 153	2.95	141.97	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 153	2.95	0	Ionic (Protein Cationic)	false
O2P	NZ	LYS- 153	3.65	0	Ionic (Protein Cationic)	false
O2A	CZ	ARG- 156	3.62	0	Ionic (Protein Cationic)	false
O2P	CZ	ARG- 156	3.87	0	Ionic (Protein Cationic)	false
O2A	NE	ARG- 156	2.88	148.93	H-Bond (Protein Donor)	false
O2P	NH2	ARG- 156	2.88	142.91	H-Bond (Protein Donor)	false
C1'	CB	HIS- 188	3.69	0	Hydrophobic	false
C9A	CB	HIS- 188	3.64	0	Hydrophobic	false
O2	NE2	GLN- 189	2.99	154.44	H-Bond (Protein Donor)	false
O4	N	THR- 190	3.18	153.3	H-Bond (Protein Donor)	false
C6	CG	GLU- 257	4.02	0	Hydrophobic	false
C7M	CG	GLU- 257	4.29	0	Hydrophobic	false
C1B	CB	ALA- 320	4.35	0	Hydrophobic	false
N3A	NE2	HIS- 325	2.83	157.52	H-Bond (Protein Donor)	false
C1B	CG2	VAL- 326	4.36	0	Hydrophobic	false
O3B	O	ASP- 386	3.28	136.91	H-Bond (Ligand Donor)	false
O1P	N	GLY- 390	2.92	157.17	H-Bond (Protein Donor)	false
C7M	CG2	VAL- 393	4.08	0	Hydrophobic	false
C8M	CG2	VAL- 393	3.86	0	Hydrophobic	false
C7M	CG2	THR- 394	4.02	0	Hydrophobic	false
C7M	CG1	VAL- 450	3.82	0	Hydrophobic	false
C8M	CG2	THR- 454	4.3	0	Hydrophobic	false
C7M	CB	GLU- 455	3.81	0	Hydrophobic	false
C7	CG	GLU- 455	3.52	0	Hydrophobic	false
C4'	CB	HIS- 458	3.99	0	Hydrophobic	false
C2B	CB	SER- 462	4.07	0	Hydrophobic	false
O2B	O	HOH- 6027	3.02	179.98	H-Bond (Protein Donor)	false
O4B	O	HOH- 6403	3.05	157.45	H-Bond (Protein Donor)	false