scPDB - 4h4u entry

Protein Data Bank Entry:

PDB ID : 4h4u

Resolution :1.600 Å

Experimental Method : X-ray

Deposition Date : 2012-09-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Biphenyl dioxygenase ferredoxin reductase subunit
ID:	E7FJB9_9BURK
AC:	E7FJB9
Organism:	Acidovorax sp. KKS102
Reign:	Bacteria
TaxID:	358220
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	21.820
Number of residues:	46
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	1
Water Molecules:	4
Cofactors:	FAD
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.142	968.625

% Hydrophobic	% Polar
47.74	52.26
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	55.75 %
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
71.5431	24.3109	10.8535

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
C4D	CG2	VAL- 155	4.26	0	Hydrophobic	false
O2N	N	ILE- 156	3.31	158.65	H-Bond (Protein Donor)	false
C4D	CD1	ILE- 156	3.65	0	Hydrophobic	false
O3B	OE1	GLU- 175	2.75	150.91	H-Bond (Ligand Donor)	false
O3B	OE2	GLU- 175	3.42	125.26	H-Bond (Ligand Donor)	false
O1X	NH2	ARG- 176	3.16	134.35	H-Bond (Protein Donor)	false
O1X	NE	ARG- 176	3.13	136.79	H-Bond (Protein Donor)	false
O1X	CZ	ARG- 176	3.53	0	Ionic (Protein Cationic)	false
O2X	CZ	ARG- 176	3.45	0	Ionic (Protein Cationic)	false
DuAr	CZ	ARG- 176	3.54	169.75	Pi/Cation	false
O3X	NE2	GLN- 177	3.25	137.8	H-Bond (Protein Donor)	false
C4N	CB	ALA- 184	3.66	0	Hydrophobic	false
C1B	CB	ILE- 235	4.22	0	Hydrophobic	false
O1N	N	GLY- 236	3.17	134.53	H-Bond (Protein Donor)	false
C5D	CG1	VAL- 237	4.34	0	Hydrophobic	false
O2D	O	GLU- 289	3.12	133.54	H-Bond (Ligand Donor)	false
C3N	CB	GLU- 289	4.37	0	Hydrophobic	false
C2D	CB	GLU- 289	3.82	0	Hydrophobic	false
C3N	CG2	THR- 290	3.92	0	Hydrophobic	false
C5N	CE2	TYR- 319	3.37	0	Hydrophobic	false
O2D	O2'	FAD- 502	3.26	130.01	H-Bond (Ligand Donor)	false
O1A	O	HOH- 656	2.83	179.96	H-Bond (Protein Donor)	false
O2N	O	HOH- 722	3.17	179.96	H-Bond (Protein Donor)	false
N3A	O	HOH- 740	3.14	179.99	H-Bond (Protein Donor)	false