scPDB - 2c9e entry

Protein Data Bank Entry:

PDB ID : 2c9e

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2005-12-09

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Peridinin-chlorophyll a protein, high-salt form
ID:	O76183_AMPCA
AC:	O76183
Organism:	Amphidinium carterae
Reign:	Eukaryota
TaxID:	2961
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	26.709
Number of residues:	51
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	4
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.562	729.000

% Hydrophobic	% Polar
61.11	38.89
According to VolSite

Ligand :

HET Code:	PID
Formula:	C39H50O7
Molecular weight:	630.810 g/mol
DrugBank ID:	DB03001
Buried Surface Area:	52.62 %
Polar Surface area:	105.59 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	2
Rings:	4
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
13.1975	13.6881	11.0421

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
C27	CB	TRP- 23	4.49	0	Hydrophobic	false
C28	CD2	TRP- 23	3.45	0	Hydrophobic	false
C31	CB	TRP- 23	4.24	0	Hydrophobic	false
CM5	CZ3	TRP- 23	4.25	0	Hydrophobic	false
CM8	CE2	TRP- 23	3.63	0	Hydrophobic	false
CM6	CB	ALA- 73	4.44	0	Hydrophobic	false
CM7	CB	ALA- 73	3.9	0	Hydrophobic	false
CM7	CD2	LEU- 74	3.91	0	Hydrophobic	false
CM7	CB	ALA- 77	3.68	0	Hydrophobic	false
C31	CD1	LEU- 83	3.61	0	Hydrophobic	false
O5	O	LEU- 83	2.95	156.67	H-Bond (Ligand Donor)	false
CM8	CE	MET- 84	4.03	0	Hydrophobic	false
CM7	CB	ALA- 85	3.9	0	Hydrophobic	false
O5	N	ALA- 85	2.92	143.1	H-Bond (Protein Donor)	false
CM8	CE1	PHE- 90	4.17	0	Hydrophobic	false
CM2	CG2	ILE- 101	4.29	0	Hydrophobic	false
CM3	CG2	ILE- 101	4.01	0	Hydrophobic	false
CM4	CD1	ILE- 101	4.3	0	Hydrophobic	false
C4	CG	LYS- 106	3.89	0	Hydrophobic	false
CM3	CG	LYS- 106	4.27	0	Hydrophobic	false
C6	CD1	PHE- 109	4.47	0	Hydrophobic	false
CM3	CD1	PHE- 109	3.69	0	Hydrophobic	false
C3	CB	ALA- 110	3.9	0	Hydrophobic	false
CM4	CD1	LEU- 145	3.92	0	Hydrophobic	false
CM1	CB	THR- 146	3.59	0	Hydrophobic	false
CM2	CG1	VAL- 149	3.51	0	Hydrophobic	false
C4	CG	ARG- 150	4.12	0	Hydrophobic	false
CM2	CB	ARG- 150	4.07	0	Hydrophobic	false