scPDB - 2ght entry

Protein Data Bank Entry:

PDB ID : 2ght

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2006-03-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1
ID:	CTDS1_HUMAN
AC:	Q9GZU7
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.1.3.16

Chains:

Chain Name:	Percentage of Residues within binding site
A	94 %
B	6 %

Ligand binding site composition:

B-Factor:	26.101
Number of residues:	32
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.267	357.750

% Hydrophobic	% Polar
52.83	47.17
According to VolSite

Ligand :

HET Code:	SER_PRO_THR_PRO_SEP
Formula:	C20H33N5O11P
Molecular weight:	550.477 g/mol
DrugBank ID:	-
Buried Surface Area:	49.61 %
Polar Surface area:	266.21 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	5
Rings:	2
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
36.8109	-2.59046	-1.49216

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
CB	CB	ALA- 85	3.31	0	Hydrophobic	false
O1P	ND2	ASN- 96	2.58	159.35	H-Bond (Protein Donor)	false
O3P	ND2	ASN- 96	3.42	137.06	H-Bond (Protein Donor)	false
O2P	N	LEU- 97	3.34	138.62	H-Bond (Protein Donor)	false
N	OD2	ASP- 98	3.08	158.99	H-Bond (Ligand Donor)	false
CB	CB	ASP- 98	4.02	0	Hydrophobic	false
O2P	N	ASP- 98	2.91	149.3	H-Bond (Protein Donor)	false
CG	CZ	PHE- 106	3.56	0	Hydrophobic	false
CB	CG1	VAL- 118	4.13	0	Hydrophobic	false
CG	CD1	ILE- 120	4.41	0	Hydrophobic	false
O2P	OG1	THR- 152	2.55	155.34	H-Bond (Protein Donor)	false
CB	CB	ALA- 153	4.22	0	Hydrophobic	false
O1P	N	ALA- 153	2.89	159.45	H-Bond (Protein Donor)	false
O	N	LEU- 155	2.63	164.31	H-Bond (Protein Donor)	false
CB	CD1	LEU- 155	4.02	0	Hydrophobic	false
CB	CD	LYS- 157	4.39	0	Hydrophobic	false
CB	CB	TYR- 158	4.13	0	Hydrophobic	false
CG2	CE2	TYR- 158	3.95	0	Hydrophobic	false
O	NH2	ARG- 178	2.68	163.14	H-Bond (Protein Donor)	false
O	NH1	ARG- 178	3.22	131.5	H-Bond (Protein Donor)	false
CG	CD2	TYR- 188	3.72	0	Hydrophobic	false
O1P	NZ	LYS- 190	3.03	171.59	H-Bond (Protein Donor)	false
O1P	NZ	LYS- 190	3.03	0	Ionic (Protein Cationic)	false
O3P	MG	MG- 257	2.2	0	Metal Acceptor	false