scPDB - 1m1d entry

Protein Data Bank Entry:

PDB ID : 1m1d

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2002-06-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	HAT A1
ID:	Q27198_TETTH
AC:	Q27198
Organism:	Tetrahymena thermophila
Reign:	Eukaryota
TaxID:	5911
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	27.545
Number of residues:	45
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.351	526.500

% Hydrophobic	% Polar
42.31	57.69
According to VolSite

Ligand :

HET Code:	LYX
Formula:	C30H48N9O19P3S
Molecular weight:	963.737 g/mol
DrugBank ID:	-
Buried Surface Area:	50.45 %
Polar Surface area:	509.48 Å2

Number of
H-Bond Acceptors:	24
H-Bond Donors:	7
Rings:	3
Aromatic rings:	2
Anionic atoms:	5
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	27

Mass center Coordinates

X	Y	Z
34.394	0.951607	34.101

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
C15	CB	GLN- 376	3.56	0	Hydrophobic	false
C15	CD2	LEU- 377	3.57	0	Hydrophobic	false
S20	CD2	LEU- 377	3.85	0	Hydrophobic	false
C22	CG1	VAL- 423	3.4	0	Hydrophobic	false
C9	CG	LEU- 426	3.72	0	Hydrophobic	false
C19	CB	LEU- 426	4.16	0	Hydrophobic	false
C22	CB	LEU- 426	3.34	0	Hydrophobic	false
N17	O	LEU- 426	2.8	138.12	H-Bond (Ligand Donor)	false
C15	CB	ALA- 427	4.12	0	Hydrophobic	false
C9	CG2	VAL- 428	4.33	0	Hydrophobic	false
C10	CB	VAL- 428	4.39	0	Hydrophobic	false
O35	N	VAL- 428	2.63	158.68	H-Bond (Protein Donor)	false
C10	CG	GLN- 433	4.31	0	Hydrophobic	false
O36	N	VAL- 434	2.74	176.5	H-Bond (Protein Donor)	false
O37	N	GLY- 438	2.76	152.32	H-Bond (Protein Donor)	false
O38	OG1	THR- 439	3.31	167.16	H-Bond (Protein Donor)	false
NZ	O	TYR- 460	2.62	164.97	H-Bond (Ligand Donor)	false
CB	CB	ASP- 462	3.76	0	Hydrophobic	false
N60	O	PHE- 464	2.81	162.14	H-Bond (Ligand Donor)	false
C19	CB	ALA- 465	4	0	Hydrophobic	false
C6	CE1	TYR- 468	3.69	0	Hydrophobic	false
C8	CG	TYR- 468	4.03	0	Hydrophobic	false
C9	CE2	TYR- 468	4.44	0	Hydrophobic	false
C40	CE1	TYR- 468	4.26	0	Hydrophobic	false
C50	CD1	TYR- 468	4.24	0	Hydrophobic	false
C19	CE1	PHE- 469	3.67	0	Hydrophobic	false
C22	CZ	PHE- 469	3.69	0	Hydrophobic	false
N	OD1	ASP- 491	3.22	131.6	H-Bond (Ligand Donor)	false
N	OD1	ASP- 491	3.22	0	Ionic (Ligand Cationic)	false
O37	O	HOH- 648	2.67	158.95	H-Bond (Protein Donor)	false