scPDB - 3ms5 entry

Protein Data Bank Entry:

PDB ID : 3ms5

Resolution :1.820 Å

Experimental Method : X-ray

Deposition Date : 2010-04-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	4.800	4.800	4.800	0.000	4.800	1

List of CHEMBLId :

CHEMBL2104708

Binding Site :

Uniprot Annotation

Name:	Gamma-butyrobetaine dioxygenase
ID:	BODG_HUMAN
AC:	O75936
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	1.14.11.1

Chains:

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

Ligand binding site composition:

B-Factor:	15.571
Number of residues:	21
Including
Standard Amino Acids:	21
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.916	465.750

% Hydrophobic	% Polar
48.55	51.45
According to VolSite

Ligand :

HET Code:	REE
Formula:	C6H14N2O2
Molecular weight:	146.188 g/mol
DrugBank ID:	-
Buried Surface Area:	72.2 %
Polar Surface area:	52.16 Å2

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

Mass center Coordinates

X	Y	Z
21.9606	29.8059	87.6959

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
O1	ND2	ASN- 191	2.93	155.87	H-Bond (Protein Donor)	false
C2	CB	ASP- 204	3.94	0	Hydrophobic	false
O2	N	TYR- 205	2.76	150.68	H-Bond (Protein Donor)	false
O2	ND2	ASN- 292	2.78	147.88	H-Bond (Protein Donor)	false
N1	OH	TYR- 366	3.32	162.18	H-Bond (Ligand Donor)	false