scPDB - 1d6h entry

Protein Data Bank Entry:

PDB ID : 1d6h

Resolution :2.150 Å

Experimental Method : X-ray

Deposition Date : 1999-10-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Chalcone synthase 2
ID:	CHS2_MEDSA
AC:	P30074
Organism:	Medicago sativa
Reign:	Eukaryota
TaxID:	3879
EC Number:	2.3.1.74

Chains:

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

Ligand binding site composition:

B-Factor:	38.719
Number of residues:	32
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.483	435.375

% Hydrophobic	% Polar
72.09	27.91
According to VolSite

Ligand :

HET Code:	COA
Formula:	C21H32N7O16P3S
Molecular weight:	763.502 g/mol
DrugBank ID:	DB01992
Buried Surface Area:	44.01 %
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
6.13779	53.5901	47.1898

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
O9A	NZ	LYS- 55	3.75	0	Ionic (Protein Cationic)	false
O7A	NH2	ARG- 58	3.18	149.87	H-Bond (Protein Donor)	false
O8A	NE	ARG- 58	2.64	129.73	H-Bond (Protein Donor)	false
O7A	CZ	ARG- 58	3.81	0	Ionic (Protein Cationic)	false
O8A	CZ	ARG- 58	3.64	0	Ionic (Protein Cationic)	false
C1B	CE	MET- 59	3.41	0	Hydrophobic	false
CEP	CG	MET- 59	4.48	0	Hydrophobic	false
C4B	CG	MET- 59	3.53	0	Hydrophobic	false
C5B	CE	LYS- 62	3.5	0	Hydrophobic	false
CCP	CB	LYS- 62	3.54	0	Hydrophobic	false
CDP	CB	LYS- 62	4.39	0	Hydrophobic	false
O1A	NZ	LYS- 62	3.05	127.38	H-Bond (Protein Donor)	false
CDP	CB	SER- 63	4.26	0	Hydrophobic	false
CEP	CG2	VAL- 210	4.11	0	Hydrophobic	false
CDP	CD2	LEU- 214	4.32	0	Hydrophobic	false
C2P	CE1	PHE- 215	4.1	0	Hydrophobic	false
S1P	CZ	PHE- 215	3.76	0	Hydrophobic	false
S1P	CG2	ILE- 254	4.35	0	Hydrophobic	false
S1P	CD2	LEU- 267	3.37	0	Hydrophobic	false
C6P	CG	PRO- 272	3.55	0	Hydrophobic	false
CDP	CG	PRO- 307	3.91	0	Hydrophobic	false
CAP	CB	ALA- 308	3.89	0	Hydrophobic	false
O9P	N	ALA- 308	3.15	163.43	H-Bond (Protein Donor)	false