scPDB - 5ccb entry

Protein Data Bank Entry:

PDB ID : 5ccb

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2015-07-01

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A
ID:	TRM61_HUMAN
AC:	Q96FX7
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.1.1.220

Chains:

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

Ligand binding site composition:

B-Factor:	38.811
Number of residues:	37
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.158	428.625

% Hydrophobic	% Polar
47.24	52.76
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	77.13 %
Polar Surface area:	212.38 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
-41.0108	-39.441	22.7872

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
CB	CB	THR- 84	4.48	0	Hydrophobic	false
SD	CB	THR- 84	3.72	0	Hydrophobic	false
C3'	CG2	THR- 84	4.08	0	Hydrophobic	false
O	N	LEU- 87	3.29	171.8	H-Bond (Protein Donor)	false
OXT	N	SER- 114	2.92	144.83	H-Bond (Protein Donor)	false
OXT	N	SER- 116	3.06	157.43	H-Bond (Protein Donor)	false
O3'	OE1	GLU- 135	2.73	165.3	H-Bond (Ligand Donor)	false
O3'	OE2	GLU- 135	3.38	127.74	H-Bond (Ligand Donor)	false
O2'	OE2	GLU- 135	2.53	149.77	H-Bond (Ligand Donor)	false
N3	N	PHE- 136	3.25	146.41	H-Bond (Protein Donor)	false
DuAr	DuAr	PHE- 136	3.49	0	Aromatic Face/Face	false
C2'	CE1	PHE- 136	3.78	0	Hydrophobic	false
O3'	NE	ARG- 140	2.98	143.74	H-Bond (Protein Donor)	false
O2'	NH2	ARG- 140	2.88	177.57	H-Bond (Protein Donor)	false
N6	OD1	ASP- 163	2.91	155.57	H-Bond (Ligand Donor)	false
N1	N	VAL- 164	3.14	166.73	H-Bond (Protein Donor)	false
N	OD2	ASP- 181	2.84	168.64	H-Bond (Ligand Donor)	false
N	OD2	ASP- 181	2.84	0	Ionic (Ligand Cationic)	false
CG	CB	ASP- 181	4.43	0	Hydrophobic	false
C1'	CG2	ILE- 182	4.47	0	Hydrophobic	false
N	O	HOH- 441	2.79	176.12	H-Bond (Ligand Donor)	false