Chemical Components in the PDB

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EDU : Summary

Code

EDU

One-letter code

X

Molecule name

2'-deoxy-5-ethynyluridine

Systematic names

ProgramVersionName
ACDLabs 12.01 2'-deoxy-5-ethynyluridine
OpenEye OEToolkits 1.7.6 5-ethynyl-1-[(2R,4S,5R)-5-(hydroxymethyl)-4-oxidanyl-oxolan-2-yl]pyrimidine-2,4-dione

Formula

C11 H12 N2 O5

Formal charge

0

Molecular weight

252.223 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C1NC(=O)N(C=C1C#C)C2OC(C(O)C2)CO
SMILES CACTVS 3.385 OC[CH]1O[CH](C[CH]1O)N2C=C(C#C)C(=O)NC2=O
SMILES OpenEye OEToolkits 1.7.6 C#CC1=CN(C(=O)NC1=O)C2CC(C(O2)CO)O
Canonical SMILES CACTVS 3.385 OC[C@H]1O[C@H](C[C@@H]1O)N2C=C(C#C)C(=O)NC2=O
Canonical SMILES OpenEye OEToolkits 1.7.6 C#CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO)O

IUPAC InChI

InChI=1S/C11H12N2O5/c1-2-6-4-13(11(17)12-10(6)16)9-3-7(15)8(5-14)18-9/h1,4,7-9,14-15H,3,5H2,(H,12,16,17)/t7-,8+,9+/m0/s1

IUPAC InChI key

CDEURGJCGCHYFH-DJLDLDEBSA-N
EDU

wwPDB Information

Atom count

30 (18 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2014-02-12

Last modified at

2014-08-08

Status

Released

Obsoleted

Not Assigned



EDU : Atoms of Molecule

Total Number of Atoms: 30
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O01 O O01 N N N 0 -4.072 -1.243 2.012
2 C03 C C03 N N N 0 -3.928 -0.914 0.629
3 C06 C C06 R N N 0 -2.951 0.254 0.481
4 O08 O O08 N N N 0 -1.609 -0.17 0.806
5 C09 C C09 S N N 0 -2.875 0.708 -0.994
6 O10 O O10 N N N 0 -3.707 1.849 -1.209
7 C13 C C13 N N N 0 -1.388 1.075 -1.198
8 C16 C C16 R N N 0 -0.741 0.799 0.178
9 N18 N N18 N N N 0 0.604 0.245 0.007
10 C19 C C19 N N N 0 0.755 -0.93 -0.625
11 O20 O O20 N N N 0 -0.231 -1.508 -1.04
12 N21 N N21 N N N 0 1.965 -1.486 -0.811
13 C23 C C23 N N N 0 3.076 -0.867 -0.36
14 O24 O O24 N N N 0 4.175 -1.365 -0.526
15 C25 C C25 N N N 0 2.933 0.421 0.335
16 C26 C C26 N N N 0 1.678 0.937 0.488
17 C28 C C28 N N N 0 4.08 1.118 0.832
18 C29 C C29 N N N 0 5.021 1.69 1.24
19 H1 H H1 N N N 0 -4.678 -1.976 2.181
20 H2 H H2 N N N 0 -3.545 -1.78 0.088
21 H3 H H3 N N N 0 -4.898 -0.631 0.22
22 H4 H H4 N N N 0 -3.253 1.084 1.119
23 H5 H H5 N N N 0 -3.162 -0.106 -1.659
24 H6 H H6 N N N 0 -3.697 2.177 -2.119
25 H7 H H7 N N N 0 -0.94 0.443 -1.964
26 H8 H H8 N N N 0 -1.288 2.127 -1.465
27 H9 H H9 N N N 0 -0.703 1.714 0.769
28 H10 H H10 N N N 0 2.039 -2.337 -1.271
29 H11 H H11 N N N 0 1.535 1.881 0.993
30 H12 H H12 N N N 0 5.862 2.202 1.605



EDU : Chemical Bonds

Total Number of Bonds: 31
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C29 C28 C C trip 1.17 N N
2 C28 C25 C C sing 1.43 N N
3 O24 C23 O C doub 1.22 N N
4 C25 C23 C C sing 1.47 N N
5 C25 C26 C C doub 1.37 N N
6 C23 N21 C N sing 1.35 N N
7 C03 O01 C O sing 1.43 N N
8 C03 C06 C C sing 1.53 N N
9 C26 N18 C N sing 1.37 N N
10 O08 C06 O C sing 1.44 N N
11 O08 C16 O C sing 1.44 N N
12 N21 C19 N C sing 1.34 N N
13 C06 C09 C C sing 1.55 N N
14 N18 C19 N C sing 1.34 N N
15 N18 C16 N C sing 1.46 N N
16 C19 O20 C O doub 1.22 N N
17 C16 C13 C C sing 1.55 N N
18 C09 C13 C C sing 1.55 N N
19 C09 O10 C O sing 1.43 N N
20 O01 H1 O H sing 0.97 N N
21 C03 H2 C H sing 1.09 N N
22 C03 H3 C H sing 1.09 N N
23 C06 H4 C H sing 1.09 N N
24 C09 H5 C H sing 1.09 N N
25 O10 H6 O H sing 0.97 N N
26 C13 H7 C H sing 1.09 N N
27 C13 H8 C H sing 1.09 N N
28 C16 H9 C H sing 1.09 N N
29 N21 H10 N H sing 0.97 N N
30 C26 H11 C H sing 1.08 N N
31 C29 H12 C H sing 1.05 N N



EDU : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
EDU 4oqn Open in New Window Bound ligand 2 1