scPDB - 4jn9 entry

Protein Data Bank Entry:

PDB ID : 4jn9

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2013-03-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	DepH
ID:	A4ZPY8_CHRVL
AC:	A4ZPY8
Organism:	Chromobacterium violaceum
Reign:	Bacteria
TaxID:	536
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	17.755
Number of residues:	67
Including
Standard Amino Acids:	60
Non Standard Amino Acids:	1
Water Molecules:	6
Cofactors:
Metals:	CL

Cavity properties

Ligandability	Volume (Å3)
1.293	999.000

% Hydrophobic	% Polar
44.26	55.74
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	75.28 %
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
49.15	-1.42011	26.2664

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	OG	SER- 57	2.74	152.73	H-Bond (Protein Donor)	false
C5B	CB	SER- 57	3.91	0	Hydrophobic	false
O1P	N	ALA- 59	2.95	160.27	H-Bond (Protein Donor)	false
O3B	OD1	ASP- 78	2.82	160.32	H-Bond (Ligand Donor)	false
N3A	N	ALA- 79	3.19	136.63	H-Bond (Protein Donor)	false
C1B	CB	ALA- 79	4.37	0	Hydrophobic	false
O3B	N	ALA- 81	3.36	123.33	H-Bond (Protein Donor)	false
O2B	N	ALA- 81	2.92	158.36	H-Bond (Protein Donor)	false
O1A	N	ARG- 83	3.02	140.71	H-Bond (Protein Donor)	false
C3'	CD	ARG- 83	4.47	0	Hydrophobic	false
C8M	CG	ARG- 83	3.75	0	Hydrophobic	false
C6	CB	ASN- 84	4.46	0	Hydrophobic	false
C9A	CB	ASN- 84	4.06	0	Hydrophobic	false
C7M	CB	PHE- 86	4.43	0	Hydrophobic	false
C6	CB	ALA- 87	4.16	0	Hydrophobic	false
N3	O	HIS- 91	2.81	155.19	H-Bond (Ligand Donor)	false
O4	N	HIS- 91	2.79	162.79	H-Bond (Protein Donor)	false
N6A	O	VAL- 125	3.07	164.28	H-Bond (Ligand Donor)	false
N1A	N	VAL- 125	3.03	167.61	H-Bond (Protein Donor)	false
C7M	CE2	TRP- 170	4.26	0	Hydrophobic	false
C8M	CZ2	TRP- 170	3.76	0	Hydrophobic	false
N5	NE2	HIS- 181	2.89	141.79	H-Bond (Protein Donor)	false
O3'	OD1	ASP- 311	2.87	167.34	H-Bond (Ligand Donor)	false
C5'	CB	ASP- 311	4.4	0	Hydrophobic	false
O2P	N	ASP- 311	3	162.91	H-Bond (Protein Donor)	false
O2	N	VAL- 319	2.7	164.58	H-Bond (Protein Donor)	false
C4'	CG2	VAL- 319	4.2	0	Hydrophobic	false
C5'	CB	ALA- 322	4.41	0	Hydrophobic	false
O2P	O	HOH- 503	2.79	179.99	H-Bond (Protein Donor)	false
O1P	O	HOH- 509	2.6	171.38	H-Bond (Protein Donor)	false