scPDB - 2d3m entry

Protein Data Bank Entry:

PDB ID : 2d3m

Resolution :1.600 Å

Experimental Method : X-ray

Deposition Date : 2005-09-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	5,7-dihydroxy-2-methylchromone synthase
ID:	PCS_ALOAR
AC:	Q58VP7
Organism:	Aloe arborescens
Reign:	Eukaryota
TaxID:	45385
EC Number:	2.3.1.216

Chains:

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

Ligand binding site composition:

B-Factor:	17.159
Number of residues:	37
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.416	567.000

% Hydrophobic	% Polar
67.86	32.14
According to VolSite

Ligand :

HET Code:	COA
Formula:	C21H32N7O16P3S
Molecular weight:	763.502 g/mol
DrugBank ID:	DB01992
Buried Surface Area:	51.8 %
Polar Surface area:	426.11 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	6
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	18

Mass center Coordinates

X	Y	Z
6.41833	28.6079	-25.4231

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
O7A	NZ	LYS- 68	3.43	130.23	H-Bond (Protein Donor)	false
O7A	NZ	LYS- 68	3.43	0	Ionic (Protein Cationic)	false
CEP	CG2	ILE- 72	3.97	0	Hydrophobic	false
C5B	CG1	ILE- 72	3.97	0	Hydrophobic	false
O1A	NZ	LYS- 75	3.89	0	Ionic (Protein Cationic)	false
CCP	CB	LYS- 75	4.31	0	Hydrophobic	false
CDP	CG2	THR- 76	3.99	0	Hydrophobic	false
S1P	CB	CSD- 177	4.45	0	Hydrophobic	false
CEP	CG2	ILE- 223	3.6	0	Hydrophobic	false
C6P	CD1	LEU- 227	3.91	0	Hydrophobic	false
S1P	CZ	PHE- 228	3.55	0	Hydrophobic	false
C2P	CD1	ILE- 267	3.59	0	Hydrophobic	false
S1P	CG2	ILE- 267	4.34	0	Hydrophobic	false
C2P	CZ	PHE- 278	4.15	0	Hydrophobic	false
S1P	CE1	PHE- 278	3.66	0	Hydrophobic	false
N6A	O	LEU- 280	3.21	161.06	H-Bond (Ligand Donor)	false
C6P	CD2	LEU- 280	3.71	0	Hydrophobic	false
C2P	CD1	LEU- 280	3.74	0	Hydrophobic	false
O2B	NZ	LYS- 282	3.26	155.1	H-Bond (Protein Donor)	false
O5P	OG	SER- 284	2.87	151.72	H-Bond (Protein Donor)	false
O4A	CZ	ARG- 323	3.2	0	Ionic (Protein Cationic)	false
O4A	NH2	ARG- 323	2.77	139.98	H-Bond (Protein Donor)	false
O4A	NH1	ARG- 323	2.82	137.36	H-Bond (Protein Donor)	false
O6A	NH1	ARG- 323	2.95	145.06	H-Bond (Protein Donor)	false
CAP	CB	ALA- 324	3.8	0	Hydrophobic	false
O9P	N	ALA- 324	3	161.07	H-Bond (Protein Donor)	false