scPDB - 5eom entry

Protein Data Bank Entry:

PDB ID : 5eom

Resolution :2.550 Å

Experimental Method : X-ray

Deposition Date : 2015-11-10

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Putative nucleotidyltransferase MAB21L1
ID:	MB211_HUMAN
AC:	Q13394
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	76.886
Number of residues:	27
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.892	1582.875

% Hydrophobic	% Polar
37.74	62.26
According to VolSite

Ligand :

HET Code:	CTP
Formula:	C9H12N3O14P3
Molecular weight:	479.125 g/mol
DrugBank ID:	DB02431
Buried Surface Area:	57.82 %
Polar Surface area:	308.95 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	3
Rings:	2
Aromatic rings:	0
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
161.827	2.65345	52.1844

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
O2A	NH1	ARG- 23	3.24	135.44	H-Bond (Protein Donor)	false
O2A	NH2	ARG- 23	2.87	154.64	H-Bond (Protein Donor)	false
O3A	NH1	ARG- 23	2.78	154.29	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 23	3.48	0	Ionic (Protein Cationic)	false
C5'	CG	LYS- 24	4.36	0	Hydrophobic	false
C3'	CB	LYS- 24	4.36	0	Hydrophobic	false
O1B	NZ	LYS- 24	3.99	0	Ionic (Protein Cationic)	false
O1G	NZ	LYS- 24	3.28	0	Ionic (Protein Cationic)	false
O1G	NZ	LYS- 24	3.28	158.33	H-Bond (Protein Donor)	false
C5'	CG2	ILE- 27	3.98	0	Hydrophobic	false
C1'	CD1	ILE- 31	3.6	0	Hydrophobic	false
O2G	CZ	ARG- 62	3.97	0	Ionic (Protein Cationic)	false
O3G	CZ	ARG- 62	3.12	0	Ionic (Protein Cationic)	false
O3G	NH2	ARG- 62	2.71	131.81	H-Bond (Protein Donor)	false
O3G	NH1	ARG- 62	2.79	128.95	H-Bond (Protein Donor)	false
N3	N	TYR- 63	3.08	171.54	H-Bond (Protein Donor)	false
N4	O	TYR- 63	2.84	147.88	H-Bond (Ligand Donor)	false
N4	O	LEU- 66	3.19	140.57	H-Bond (Ligand Donor)	false
O1A	NZ	LYS- 255	2.83	131.18	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 255	2.8	154.96	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 255	2.83	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 255	3.28	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 255	2.8	0	Ionic (Protein Cationic)	false