Chemical Components in the PDB

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BRU : Summary

Code

BRU

One-letter code

U

Molecule name

5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE

Systematic names

ProgramVersionName
ACDLabs 10.04 5-bromo-2'-deoxyuridine 5'-(dihydrogen phosphate)
OpenEye OEToolkits 1.5.0 [(2R,3S,5R)-5-(5-bromo-2,4-dioxo-pyrimidin-1-yl)-3-hydroxy-oxolan-2-yl]methyl dihydrogen phosphate

Formula

C9 H12 Br N2 O8 P

Formal charge

0

Molecular weight

387.078 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 BrC=1C(=O)NC(=O)N(C=1)C2OC(C(O)C2)COP(=O)(O)O
SMILES CACTVS 3.341 O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=C(Br)C(=O)NC2=O
SMILES OpenEye OEToolkits 1.5.0 C1C(C(OC1N2C=C(C(=O)NC2=O)Br)COP(=O)(O)O)O
Canonical SMILES CACTVS 3.341 O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=C(Br)C(=O)NC2=O
Canonical SMILES OpenEye OEToolkits 1.5.0 C1[C@@H]([C@H](O[C@H]1N2C=C(C(=O)NC2=O)Br)COP(=O)(O)O)O

IUPAC InChI

InChI=1S/C9H12BrN2O8P/c10-4-2-12(9(15)11-8(4)14)7-1-5(13)6(20-7)3-19-21(16,17)18/h2,5-7,13H,1,3H2,(H,11,14,15)(H2,16,17,18)/t5-,6+,7+/m0/s1

IUPAC InChI key

LHLHVDBXXZVYJT-RRKCRQDMSA-N
BRU

wwPDB Information

Atom count

33 (21 without Hydrogen)

Polymer type

Deoxy ribonucleotide

Type description

DNA LINKING

Type code

ATOMN

Is modified

Yes

Standard parent

DU

Defined at

1999-07-08

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



BRU : Atoms of Molecule

Total Number of Atoms: 33
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N1 N N1 N N N 0 0.527 -0.166 1.257
2 C2 C C2 N N N 0 0.0 -1.399 1.16
3 N3 N N3 N N N 0 -0.65 -1.958 2.198
4 C4 C C4 N N N 0 -0.792 -1.28 3.355
5 C5 C C5 N N N 0 -0.245 0.021 3.47
6 C6 C C6 N N N 0 0.405 0.555 2.414
7 O2 O O2 N N N 0 0.119 -2.023 0.123
8 O4 O O4 N N N 0 -1.384 -1.783 4.293
9 BR BR BR N N N 0 -0.427 0.998 5.078
10 C1' C C1* R N N 0 1.234 0.413 0.112
11 C2' C C2* N N N 0 2.445 -0.464 -0.271
12 C3' C C3* S N N 0 2.484 -0.397 -1.815
13 C4' C C4* R N N 0 1.29 0.512 -2.183
14 O3' O O3* N N N 0 3.711 0.183 -2.26
15 O4' O O4* N N N 0 0.388 0.407 -1.058
16 C5' C C5* N N N 0 0.609 0.016 -3.46
17 O5' O O5* N N N 0 -0.532 0.83 -3.737
18 P P P N N N 0 -1.197 0.256 -5.086
19 OP1 O O1P N N N 0 -1.595 -1.154 -4.878
20 OP2 O O2P N N N 0 -2.496 1.131 -5.459
21 OP3 O O3P N N Y 0 -0.129 0.34 -6.289
22 HN3 H HN3 N N N 0 -1.021 -2.85 2.112
23 H6 H H6 N N N 0 0.829 1.546 2.483
24 H1' H H1* N N N 0 1.558 1.428 0.341
25 H2' H 1H2* N N N 0 2.294 -1.491 0.061
26 H2'' H 2H2* N N N 0 3.363 -0.056 0.151
27 H3' H H3* N N N 0 2.354 -1.39 -2.244
28 H4' H H4* N N N 0 1.624 1.542 -2.307
29 HO3' H *HO3 N N Y 0 4.42 -0.41 -1.977
30 H5' H 1H5* N N N 0 1.309 0.077 -4.293
31 H5'' H 2H5* N N N 0 0.293 -1.017 -3.326
32 HOP2 H 2HOP N N N 0 -2.862 0.754 -6.271
33 HOP3 H 3HOP N N N 0 0.102 1.273 -6.391



BRU : Chemical Bonds

Total Number of Bonds: 34
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N1 C2 N C sing 1.34 N N
2 N1 C6 N C sing 1.37 N N
3 N1 C1' N C sing 1.46 N N
4 C2 N3 C N sing 1.35 N N
5 C2 O2 C O doub 1.22 N N
6 N3 C4 N C sing 1.35 N N
7 N3 HN3 N H sing 0.97 N N
8 C4 C5 C C sing 1.42 N N
9 C4 O4 C O doub 1.22 N N
10 C5 C6 C C doub 1.35 N N
11 C5 BR C BR sing 1.89 N N
12 C6 H6 C H sing 1.08 N N
13 C1' C2' C C sing 1.54 N N
14 C1' O4' C O sing 1.44 N N
15 C1' H1' C H sing 1.09 N N
16 C2' C3' C C sing 1.55 N N
17 C2' H2' C H sing 1.09 N N
18 C2' H2'' C H sing 1.09 N N
19 C3' C4' C C sing 1.55 N N
20 C3' O3' C O sing 1.43 N N
21 C3' H3' C H sing 1.09 N N
22 C4' O4' C O sing 1.45 N N
23 C4' C5' C C sing 1.53 N N
24 C4' H4' C H sing 1.09 N N
25 O3' HO3' O H sing 0.97 N N
26 C5' O5' C O sing 1.43 N N
27 C5' H5' C H sing 1.09 N N
28 C5' H5'' C H sing 1.09 N N
29 O5' P O P sing 1.61 N N
30 P OP1 P O doub 1.48 N N
31 P OP2 P O sing 1.61 N N
32 P OP3 P O sing 1.61 N N
33 OP2 HOP2 O H sing 0.97 N N
34 OP3 HOP3 O H sing 0.97 N N



BRU : Used in PDB Entries

Total Number of PDB Entries: 118
Ligand Code PDB Entry ID Type Total Distinct
BRU 115d Open in New Window Polymer component 4 2
BRU 165d Open in New Window Polymer component 2 1
BRU 1a35 Open in New Window Polymer component 8 8
BRU 1aio Open in New Window Polymer component 2 1
BRU 1awc Open in New Window Polymer component 3 3
BRU 1cs7 Open in New Window Polymer component 4 1
BRU 1d3r Open in New Window Polymer component 4 2
BRU 1d9r Open in New Window Polymer component 2 1
BRU 1da1 Open in New Window Polymer component 2 1
BRU 1dcr Open in New Window Polymer component 2 1
BRU 1dp7 Open in New Window Polymer component 2 2
BRU 1fn1 Open in New Window Polymer component 2 2
BRU 1fyl Open in New Window Polymer component 2 1
BRU 1gqu Open in New Window Polymer component 4 1
BRU 1i3w Open in New Window Polymer component 4 1
BRU 1iha Open in New Window Polymer component 2 1
BRU 1j6s Open in New Window Polymer component 4 1
BRU 1jpq Open in New Window Polymer component 2 1
BRU 1jxl Open in New Window Polymer component 2 2
BRU 1k3x Open in New Window Polymer component 4 4
BRU 1k8p Open in New Window Polymer component 4 2
BRU 1kdh Open in New Window Polymer component 4 4
BRU 1o27 Open in New Window Bound ligand 4 1
BRU 1p1y Open in New Window Polymer component 1 1
BRU 1p54 Open in New Window Polymer component 2 1
BRU 1r71 Open in New Window Polymer component 12 3
BRU 1sm5 Open in New Window Polymer component 4 2
BRU 1unj Open in New Window Polymer component 16 1
BRU 1unm Open in New Window Polymer component 4 1
BRU 1wtp Open in New Window Polymer component 4 1
BRU 1zet Open in New Window Polymer component 3 3
BRU 2af6 Open in New Window Bound ligand 8 1
BRU 2avj Open in New Window Polymer component 6 1
BRU 2dlj Open in New Window Polymer component 1 1
BRU 2fcc Open in New Window Polymer component 8 4
BRU 2gpx Open in New Window Polymer component 1 1
BRU 2h05 Open in New Window Polymer component 1 1
BRU 2ja5 Open in New Window Polymer component 1 1
BRU 2ja6 Open in New Window Polymer component 1 1
BRU 2ja7 Open in New Window Polymer component 2 1
BRU 2ja8 Open in New Window Polymer component 1 1
BRU 2obz Open in New Window Polymer component 2 1
BRU 2orf Open in New Window Polymer component 1 1
BRU 2org Open in New Window Polymer component 1 1
BRU 2vum Open in New Window Polymer component 1 1
BRU 2w36 Open in New Window Polymer component 4 2
BRU 2w7n Open in New Window Polymer component 6 3
BRU 344d Open in New Window Polymer component 1 1
BRU 366d Open in New Window Polymer component 1 1
BRU 3bs1 Open in New Window Polymer component 2 2
BRU 3gdd Open in New Window Polymer component 2 1
BRU 3h40 Open in New Window Polymer component 1 1
BRU 3h4b Open in New Window Polymer component 1 1
BRU 3h4d Open in New Window Polymer component 1 1
BRU 3hou Open in New Window Polymer component 2 1
BRU 3hov Open in New Window Polymer component 1 1
BRU 3how Open in New Window Polymer component 1 1
BRU 3hox Open in New Window Polymer component 1 1
BRU 3hoy Open in New Window Polymer component 1 1
BRU 3hoz Open in New Window Polymer component 1 1
BRU 3i4m Open in New Window Polymer component 1 1
BRU 3i4n Open in New Window Polymer component 1 1
BRU 3il2 Open in New Window Polymer component 8 4
BRU 3kde Open in New Window Polymer component 2 2
BRU 3lwp Open in New Window Polymer component 1 1
BRU 3ogd Open in New Window Polymer component 2 2
BRU 3oh6 Open in New Window Polymer component 2 2
BRU 3oh9 Open in New Window Polymer component 2 2
BRU 3po2 Open in New Window Polymer component 1 1
BRU 3po3 Open in New Window Polymer component 1 1
BRU 3qsc Open in New Window Polymer component 1 1
BRU 3qxr Open in New Window Polymer component 2 1
BRU 3tq6 Open in New Window Polymer component 2 1
BRU 3vaf Open in New Window Polymer component 4 2
BRU 3vag Open in New Window Polymer component 2 1
BRU 3vah Open in New Window Polymer component 2 1
BRU 3vai Open in New Window Polymer component 2 1
BRU 3vaj Open in New Window Polymer component 2 1
BRU 3vak Open in New Window Polymer component 2 1
BRU 3val Open in New Window Polymer component 4 1
BRU 3vam Open in New Window Polymer component 2 1
BRU 3vwb Open in New Window Polymer component 2 2
BRU 4a3b Open in New Window Polymer component 1 1
BRU 4a3c Open in New Window Polymer component 1 1
BRU 4a3d Open in New Window Polymer component 1 1
BRU 4a3e Open in New Window Polymer component 1 1
BRU 4a3f Open in New Window Polymer component 1 1
BRU 4a3g Open in New Window Polymer component 1 1
BRU 4a3i Open in New Window Polymer component 1 1
BRU 4a3j Open in New Window Polymer component 1 1
BRU 4a3k Open in New Window Polymer component 1 1
BRU 4a3l Open in New Window Polymer component 1 1
BRU 4a3m Open in New Window Polymer component 1 1
BRU 4a93 Open in New Window Polymer component 1 1
BRU 4bxx Open in New Window Polymer component 1 1
BRU 4by1 Open in New Window Polymer component 1 1
BRU 4by7 Open in New Window Polymer component 1 1
BRU 4e10 Open in New Window Polymer component 10 10
BRU 4g7z Open in New Window Polymer component 2 1
BRU 4i2a Open in New Window Polymer component 1 1
BRU 4nod Open in New Window Polymer component 4 1
BRU 4p5b Open in New Window Bound ligand 4 1
BRU 4rip Open in New Window Polymer component 2 2
BRU 4tu7 Open in New Window Polymer component 2 1
BRU 4tu8 Open in New Window Polymer component 2 1
BRU 4tu9 Open in New Window Polymer component 2 1
BRU 4v1m Open in New Window Polymer component 1 1
BRU 4xno Open in New Window Polymer component 2 1
BRU 5ev1 Open in New Window Polymer component 1 1
BRU 5ev2 Open in New Window Polymer component 1 1
BRU 5ev3 Open in New Window Polymer component 1 1
BRU 5ev4 Open in New Window Polymer component 1 1
BRU 5mvl Open in New Window Polymer component 2 1
BRU 5ot2 Open in New Window Polymer component 1 1
BRU 5swm Open in New Window Polymer component 1 1
BRU 5vbj Open in New Window Polymer component 2 1
BRU 5w1z Open in New Window Polymer component 4 1
BRU 5ytz Open in New Window Polymer component 2 1