scPDB - 2wd4 entry

Protein Data Bank Entry:

PDB ID : 2wd4

Resolution :1.400 Å

Experimental Method : X-ray

Deposition Date : 2009-03-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Ascorbate peroxidase
ID:	Q43758_SOYBN
AC:	Q43758
Organism:	Glycine max
Reign:	Eukaryota
TaxID:	3847
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	14.127
Number of residues:	52
Including
Standard Amino Acids:	51
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	FE

Cavity properties

Ligandability	Volume (Å3)
1.338	1161.000

% Hydrophobic	% Polar
52.03	47.97
According to VolSite

Ligand :

HET Code:	TBV
Formula:	C37H44N4O6
Molecular weight:	640.768 g/mol
DrugBank ID:	-
Buried Surface Area:	73.01 %
Polar Surface area:	165.95 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	4
Rings:	4
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	15

Mass center Coordinates

X	Y	Z
14.9093	55.4852	19.0892

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
CMD	CB	PRO- 34	4.14	0	Hydrophobic	false
CAD	CB	PRO- 34	4.14	0	Hydrophobic	false
CHD	CG	LEU- 37	4.44	0	Hydrophobic	false
CMD	CD2	LEU- 37	3.83	0	Hydrophobic	false
CBD	CD	ARG- 38	3.9	0	Hydrophobic	false
CMC	CB	ALA- 41	4.07	0	Hydrophobic	false
C47	CB	ALA- 41	3.47	0	Hydrophobic	false
CMB	CG	PRO- 132	3.7	0	Hydrophobic	false
C45	CG	PRO- 132	3.59	0	Hydrophobic	false
CHB	CB	ALA- 134	4.4	0	Hydrophobic	false
CMA	CB	ALA- 134	4	0	Hydrophobic	false
CMB	CB	ALA- 134	4.01	0	Hydrophobic	false
CMC	CE2	PHE- 145	4.11	0	Hydrophobic	false
C45	CZ	PHE- 145	3.54	0	Hydrophobic	false
C45	CE	MET- 149	4.31	0	Hydrophobic	false
CMC	CB	LEU- 159	3.97	0	Hydrophobic	false
CMD	CG1	ILE- 165	4.08	0	Hydrophobic	false
O1D	N	ALA- 167	2.92	153.29	H-Bond (Protein Donor)	false
CAA	CB	ALA- 168	3.55	0	Hydrophobic	false
O2A	N	HIS- 169	2.83	171.74	H-Bond (Protein Donor)	false
O2A	OG	SER- 173	2.72	157.09	H-Bond (Protein Donor)	false
O2A	N	SER- 173	3.01	158.19	H-Bond (Protein Donor)	false
CMA	CB	SER- 173	3.66	0	Hydrophobic	false
CBA	CB	SER- 173	3.93	0	Hydrophobic	false
CMA	CD1	PHE- 175	4.44	0	Hydrophobic	false
CAA	CH2	TRP- 179	4.34	0	Hydrophobic	false
CAD	CZ3	TRP- 179	4.2	0	Hydrophobic	false
CHB	CD1	LEU- 205	3.9	0	Hydrophobic	false
CMA	CD1	LEU- 205	4.18	0	Hydrophobic	false
CMB	CB	SER- 207	4.24	0	Hydrophobic	false
CMC	CD2	LEU- 242	4.06	0	Hydrophobic	false
NB	FE	FE- 1250	2.12	0	Metal Acceptor	false
ND	FE	FE- 1250	2.01	0	Metal Acceptor	false
DuAr	FE	FE- 1250	3.32	101.15	Pi/Cation	false
DuAr	FE	FE- 1250	3.32	81.82	Pi/Cation	false
DuAr	FE	FE- 1250	3.26	86.03	Pi/Cation	false
DuAr	FE	FE- 1250	3.26	94.51	Pi/Cation	false