scPDB - 4d5g entry

Protein Data Bank Entry:

PDB ID : 4d5g

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2014-11-04

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Cyclohexane-1,2-dione hydrolase
ID:	CHDH_AZOSP
AC:	P0CH62
Organism:	Azoarcus sp
Reign:	Bacteria
TaxID:	29544
EC Number:	3.7.1.11

Chains:

Chain Name:	Percentage of Residues within binding site
A	96 %
B	4 %

Ligand binding site composition:

B-Factor:	15.340
Number of residues:	76
Including
Standard Amino Acids:	69
Non Standard Amino Acids:	0
Water Molecules:	7
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.053	597.375

% Hydrophobic	% Polar
47.46	52.54
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	78.63 %
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
-17.8465	-41.1475	6.86606

Binding mode :

What is Poseview ?

2D View
3D View

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
O2P	N	GLY- 214	2.79	160.15	H-Bond (Protein Donor)	false
O2P	OG1	THR- 239	2.74	163.31	H-Bond (Protein Donor)	false
N1	OG	SER- 240	3.05	120.79	H-Bond (Protein Donor)	false
O2	N	SER- 240	2.93	143.77	H-Bond (Protein Donor)	false
C1'	CB	SER- 240	4.44	0	Hydrophobic	false
O1A	OG1	THR- 241	2.8	160.65	H-Bond (Protein Donor)	false
C5'	CG2	THR- 241	4.46	0	Hydrophobic	false
N3	O	ALA- 257	2.68	174.5	H-Bond (Ligand Donor)	false
C7M	CZ	PHE- 259	4.07	0	Hydrophobic	false
C6	CE1	PHE- 259	3.3	0	Hydrophobic	false
O4	N	CYS- 260	2.89	144.35	H-Bond (Protein Donor)	false
C6	SG	CYS- 260	3.88	0	Hydrophobic	false
O1P	OG	SER- 280	2.8	159.91	H-Bond (Protein Donor)	false
O2A	NE	ARG- 281	2.74	157.47	H-Bond (Protein Donor)	false
O1P	N	ARG- 281	2.93	143.84	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 281	3.75	0	Ionic (Protein Cationic)	false
C3B	CB	ARG- 281	4.25	0	Hydrophobic	false
C7M	CZ3	TRP- 285	4.2	0	Hydrophobic	false
C8M	CE3	TRP- 285	3.64	0	Hydrophobic	false
C2'	CB	TRP- 285	4.31	0	Hydrophobic	false
C9A	CB	TRP- 285	4.44	0	Hydrophobic	false
O3B	OD2	ASP- 302	2.77	160.26	H-Bond (Ligand Donor)	false
N3A	N	THR- 303	3.48	158.87	H-Bond (Protein Donor)	false
N6A	OD1	ASP- 321	2.88	177.62	H-Bond (Ligand Donor)	false
N1A	N	ALA- 322	2.97	149.39	H-Bond (Protein Donor)	false
C7M	CG2	ILE- 398	4.17	0	Hydrophobic	false
C8M	CD1	ILE- 398	3.9	0	Hydrophobic	false
C7M	CG2	THR- 402	3.93	0	Hydrophobic	false
C1'	SD	MET- 421	3.95	0	Hydrophobic	false
O2'	O	MET- 421	2.67	160.83	H-Bond (Ligand Donor)	false
C7M	CD1	LEU- 551	4.04	0	Hydrophobic	false
O2B	O	HOH- 2062	2.88	168.03	H-Bond (Protein Donor)	false
O4	O	HOH- 2185	3.49	122.37	H-Bond (Protein Donor)	false
O2'	O	HOH- 2201	2.75	160.68	H-Bond (Protein Donor)	false
O1A	O	HOH- 2268	2.63	179.96	H-Bond (Protein Donor)	false