scPDB - 4wri entry

Protein Data Bank Entry:

PDB ID : 4wri

Resolution :1.400 Å

Experimental Method : X-ray

Deposition Date : 2014-10-24

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Okadaic acid binding protein 2-alpha
ID:	Q2MHR1_HALOK
AC:	Q2MHR1
Organism:	Halichondria okadai
Reign:	Eukaryota
TaxID:	163232
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	17.049
Number of residues:	55
Including
Standard Amino Acids:	52
Non Standard Amino Acids:	3
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.607	1879.875

% Hydrophobic	% Polar
46.68	53.32
According to VolSite

Ligand :

HET Code:	OKA
Formula:	C44H67O13
Molecular weight:	803.995 g/mol
DrugBank ID:	DB02169
Buried Surface Area:	69.26 %
Polar Surface area:	185.66 Å2

Number of
H-Bond Acceptors:	13
H-Bond Donors:	4
Rings:	7
Aromatic rings:	0
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
29.4874	51.2194	57.8529

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
C17	CZ2	TRP- 22	4.03	0	Hydrophobic	false
C42	CD1	PHE- 37	3.82	0	Hydrophobic	false
C43	CG2	VAL- 41	4.03	0	Hydrophobic	false
C2	CD	ARG- 44	4.33	0	Hydrophobic	false
C43	CD	ARG- 44	4.34	0	Hydrophobic	false
C11	CD	ARG- 44	4.16	0	Hydrophobic	false
O2	NH2	ARG- 44	3.41	128.81	H-Bond (Protein Donor)	false
O2	NE	ARG- 44	2.77	158	H-Bond (Protein Donor)	false
O2	CZ	ARG- 44	3.51	0	Ionic (Protein Cationic)	false
C44	CE2	PHE- 48	3.72	0	Hydrophobic	false
C43	CE	MET- 58	3.65	0	Hydrophobic	false
C7	CD	ARG- 61	4.24	0	Hydrophobic	false
C43	CB	ARG- 61	3.87	0	Hydrophobic	false
C43	CB	SER- 62	4.07	0	Hydrophobic	false
C13	CB	HIS- 65	4.2	0	Hydrophobic	false
C18	CD2	LEU- 104	4.41	0	Hydrophobic	false
C20	CD2	LEU- 104	3.9	0	Hydrophobic	false
C6	CB	SER- 107	4.06	0	Hydrophobic	false
C21	CB	SER- 107	3.49	0	Hydrophobic	false
C21	CB	SER- 108	4.29	0	Hydrophobic	false
O11	OG	SER- 108	2.94	151.57	H-Bond (Ligand Donor)	false
C3	CD1	PHE- 111	4.02	0	Hydrophobic	false
C5	CB	PHE- 111	4.44	0	Hydrophobic	false
C26	CB	PHE- 111	4.08	0	Hydrophobic	false
C28	CD2	PHE- 111	4.25	0	Hydrophobic	false
C44	CE1	PHE- 111	4.16	0	Hydrophobic	false
C31	CE2	PHE- 111	3.85	0	Hydrophobic	false
C39	CZ3	TRP- 112	3.9	0	Hydrophobic	false
C39	CD1	ILE- 115	4.03	0	Hydrophobic	false
C33	CB	ALA- 128	4.42	0	Hydrophobic	false
C32	CD2	LEU- 131	3.76	0	Hydrophobic	false
C32	CG2	VAL- 135	4.43	0	Hydrophobic	false
C38	CG2	THR- 136	4.3	0	Hydrophobic	false
C37	CD2	LEU- 141	4.15	0	Hydrophobic	false
C37	CD1	ILE- 146	4.05	0	Hydrophobic	false
C35	CE1	PHE- 147	3.89	0	Hydrophobic	false
C37	CZ	PHE- 147	4.45	0	Hydrophobic	false
C36	CE	MET- 150	3.66	0	Hydrophobic	false
C35	CG2	THR- 163	4.15	0	Hydrophobic	false
C39	CG2	THR- 163	4.18	0	Hydrophobic	false
C29	CB	THR- 163	4.23	0	Hydrophobic	false
C18	CZ	PHE- 171	3.87	0	Hydrophobic	false
C40	CG2	VAL- 184	3.9	0	Hydrophobic	false
C36	CG2	VAL- 184	3.92	0	Hydrophobic	false
O8	NH1	ARG- 185	2.94	170.33	H-Bond (Protein Donor)	false