Chemical Components in the PDB

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UPE : Summary

Code

UPE

One-letter code

U

Molecule name

2'-deoxy-5-[(2-phenylethyl)carbamoyl]uridine 5'-(dihydrogen phosphate)

Systematic names

ProgramVersionName
ACDLabs 12.01 2'-deoxy-5-[(2-phenylethyl)carbamoyl]uridine 5'-(dihydrogen phosphate)
OpenEye OEToolkits 1.7.6 [(2R,3S,5R)-5-[2,4-bis(oxidanylidene)-5-(2-phenylethylcarbamoyl)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate

Formula

C18 H22 N3 O9 P

Formal charge

0

Molecular weight

455.356 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=P(O)(O)OCC3OC(N2C(=O)NC(=O)C(C(=O)NCCc1ccccc1)=C2)CC3O
SMILES CACTVS 3.370 O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=C(C(=O)NCCc3ccccc3)C(=O)NC2=O
SMILES OpenEye OEToolkits 1.7.6 c1ccc(cc1)CCNC(=O)C2=CN(C(=O)NC2=O)C3CC(C(O3)COP(=O)(O)O)O
Canonical SMILES CACTVS 3.370 O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=C(C(=O)NCCc3ccccc3)C(=O)NC2=O
Canonical SMILES OpenEye OEToolkits 1.7.6 c1ccc(cc1)CCNC(=O)C2=CN(C(=O)NC2=O)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O

IUPAC InChI

InChI=1S/C18H22N3O9P/c22-13-8-15(30-14(13)10-29-31(26,27)28)21-9-12(17(24)20-18(21)25)16(23)19-7-6-11-4-2-1-3-5-11/h1-5,9,13-15,22H,6-8,10H2,(H,19,23)(H,20,24,25)(H2,26,27,28)/t13-,14+,15+/m0/s1

IUPAC InChI key

CBTXGTWTWUZPNV-RRFJBIMHSA-N
UPE

wwPDB Information

Atom count

53 (31 without Hydrogen)

Polymer type

Deoxy ribonucleotide

Type description

DNA linking

Type code

ATOMN

Is modified

Yes

Standard parent

DU

Defined at

2012-11-07

Last modified at

2012-11-16

Status

Released

Obsoleted

Not Assigned



UPE : Atoms of Molecule

Total Number of Atoms: 53
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1' C C1' R N N 0 -1.927 -1.317 -0.774
2 C2 C C2 N N N 0 -0.856 -1.031 1.38
3 C2' C C2' N N N 0 -2.541 -2.695 -0.44
4 C21 C C21 N N N 0 2.911 -0.512 -0.419
5 C24 C C24 N N N 0 5.265 0.106 -0.292
6 C25 C C25 N N N 0 6.297 0.445 0.786
7 C26 C C26 N Y N 0 7.623 0.744 0.136
8 C27 C C27 N Y N 0 7.932 2.038 -0.241
9 C28 C C28 N Y N 0 9.148 2.312 -0.837
10 C29 C C29 N Y N 0 10.056 1.293 -1.057
11 C3' C C3' S N N 0 -4.065 -2.458 -0.528
12 C30 C C30 N Y N 0 9.747 -0.0010 -0.681
13 C31 C C31 N Y N 0 8.532 -0.274 -0.079
14 C4 C C4 N N N 0 1.432 -0.647 1.666
15 C4' C C4' R N N 0 -4.192 -0.966 -0.905
16 C5 C C5 N N N 0 1.592 -0.694 0.204
17 C5' C C5' N N N 0 -5.39 -0.336 -0.191
18 C6 C C6 N N N 0 0.467 -0.914 -0.566
19 H1' H H1' N N N 0 -1.677 -1.258 -1.833
20 H2' H H2' N N N 0 -2.227 -3.44 -1.172
21 H2'A H H2'A N N N 0 -2.26 -3.005 0.566
22 H24 H H24 N N N 0 5.6 -0.767 -0.853
23 H24A H H24A N N N 0 5.155 0.953 -0.969
24 H25 H H25 N N N 0 5.962 1.318 1.347
25 H25A H H25A N N N 0 6.407 -0.402 1.463
26 H27 H H27 N N N 0 7.223 2.834 -0.069
27 H28 H H28 N N N 0 9.39 3.323 -1.131
28 H29 H H29 N N N 0 11.006 1.507 -1.524
29 H3' H H3' N N N 0 -4.538 -2.651 0.435
30 H30 H H30 N N N 0 10.455 -0.798 -0.854
31 H31 H H31 N N N 0 8.293 -1.284 0.219
32 H4' H H4' N N N 0 -4.291 -0.854 -1.984
33 H5' H H5' N N N 0 -6.289 -0.911 -0.415
34 H5'A H H5'A N N N 0 -5.215 -0.341 0.885
35 H6 H H6 N N N 0 0.542 -0.956 -1.643
36 HN23 H HN23 N N N 0 3.888 -0.143 1.306
37 HN3 H HN3 N N N 0 0.072 -0.792 3.147
38 HO3' H HO3' N N N 0 -4.537 -4.23 -1.388
39 HOP2 H HOP2 N N N 0 -5.658 2.697 1.67
40 HOP3 H HOP3 N N Y 0 -7.378 3.995 -0.637
41 N1 N N1 N N N 0 -0.736 -1.078 0.044
42 N23 N N23 N N N 0 3.976 -0.185 0.34
43 N3 N N3 N N N 0 0.198 -0.82 2.186
44 O2 O O2 N N N 0 -1.955 -1.184 1.877
45 O22 O O22 N N N 0 3.042 -0.656 -1.62
46 O3' O O3' N N N 0 -4.642 -3.282 -1.544
47 O4 O O4 N N N 0 2.391 -0.456 2.391
48 O4' O O4' N N N 0 -2.962 -0.364 -0.447
49 O5' O O5' N N N 0 -5.56 1.009 -0.64
50 OP1 O OP1 N N N 0 -8.041 1.317 -0.291
51 OP2 O OP2 N N N 0 -6.5 2.266 1.469
52 OP3 O OP3 N N Y 0 -6.699 3.363 -0.912
53 P P P N N N 0 -6.729 1.974 -0.098



UPE : Chemical Bonds

Total Number of Bonds: 55
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 OP1 P O P doub 1.48 N N
2 O5' P O P sing 1.61 N N
3 OP3 P O P sing 1.61 N N
4 P OP2 P O sing 1.61 N N
5 C1' N1 C N sing 1.46 N N
6 C2 N1 C N sing 1.34 N N
7 N1 C6 N C sing 1.36 N N
8 O2 C2 O C doub 1.22 N N
9 C2 N3 C N sing 1.34 N N
10 N3 C4 N C sing 1.35 N N
11 N3 HN3 N H sing 0.97 N N
12 C4 O4 C O doub 1.22 N N
13 C4 C5 C C sing 1.47 N N
14 C6 C5 C C doub 1.38 N N
15 C5 C21 C C sing 1.47 N N
16 C6 H6 C H sing 1.08 N N
17 C2' C1' C C sing 1.55 N N
18 C1' O4' C O sing 1.44 N N
19 C1' H1' C H sing 1.09 N N
20 C2' C3' C C sing 1.54 N N
21 C2' H2' C H sing 1.09 N N
22 C2' H2'A C H sing 1.09 N N
23 C21 O22 C O doub 1.22 N N
24 C21 N23 C N sing 1.35 N N
25 N23 C24 N C sing 1.46 N N
26 N23 HN23 N H sing 0.97 N N
27 C24 C25 C C sing 1.53 N N
28 C24 H24 C H sing 1.09 N N
29 C24 H24A C H sing 1.09 N N
30 C25 C26 C C sing 1.51 N N
31 C25 H25 C H sing 1.09 N N
32 C25 H25A C H sing 1.09 N N
33 C31 C26 C C doub 1.38 N Y
34 C26 C27 C C sing 1.38 N Y
35 C27 C28 C C doub 1.38 N Y
36 C27 H27 C H sing 1.08 N N
37 C29 C28 C C sing 1.38 N Y
38 C28 H28 C H sing 1.08 N N
39 C30 C29 C C doub 1.38 N Y
40 C29 H29 C H sing 1.08 N N
41 O3' C3' O C sing 1.43 N N
42 C3' C4' C C sing 1.54 N N
43 C3' H3' C H sing 1.09 N N
44 O3' HO3' O H sing 0.97 N N
45 C31 C30 C C sing 1.38 N Y
46 C30 H30 C H sing 1.08 N N
47 C31 H31 C H sing 1.08 N N
48 C4' O4' C O sing 1.44 N N
49 C4' C5' C C sing 1.53 N N
50 C4' H4' C H sing 1.09 N N
51 C5' O5' C O sing 1.43 N N
52 C5' H5' C H sing 1.09 N N
53 C5' H5'A C H sing 1.09 N N
54 OP2 HOP2 O H sing 0.97 N N
55 OP3 HOP3 O H sing 0.97 N N



UPE : Used in PDB Entries

Total Number of PDB Entries: 4
Ligand Code PDB Entry ID Type Total Distinct
UPE 4hqu Open in New Window Polymer component 1 1
UPE 4hqx Open in New Window Polymer component 1 1
UPE 4ni7 Open in New Window Polymer component 1 1
UPE 4ni9 Open in New Window Polymer component 2 1