Chemical Components in the PDB

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H2U : Summary

Code

H2U

One-letter code

U

Molecule name

5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE

Systematic names

ProgramVersionName
ACDLabs 10.04 5'-uridylic acid
OpenEye OEToolkits 1.5.0 [(2R,3S,4R,5R)-5-(2,4-dioxo-1,3-diazinan-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl dihydrogen phosphate

Formula

C9 H15 N2 O9 P

Formal charge

0

Molecular weight

326.197 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C1N(CCC(=O)N1)C2OC(C(O)C2O)COP(=O)(O)O
SMILES CACTVS 3.341 O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2CCC(=O)NC2=O
SMILES OpenEye OEToolkits 1.5.0 C1CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O
Canonical SMILES CACTVS 3.341 O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2CCC(=O)NC2=O
Canonical SMILES OpenEye OEToolkits 1.5.0 C1CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O

IUPAC InChI

InChI=1S/C9H15N2O9P/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h4,6-8,13-14H,1-3H2,(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1

IUPAC InChI key

NBWDKGJHOHJBRJ-XVFCMESISA-N
H2U

wwPDB Information

Atom count

36 (21 without Hydrogen)

Polymer type

Ribonucleotide

Type description

RNA LINKING

Type code

ATOMN

Is modified

Yes

Standard parent

U

Defined at

1999-07-08

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



H2U : Atoms of Molecule

Total Number of Atoms: 36
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 P P P N N N 0 -1.087 0.031 -3.989
2 OP1 O O1P N N N 0 -1.678 -1.272 -3.613
3 OP2 O O2P N N N 0 -2.235 0.986 -4.593
4 OP3 O O3P N N Y 0 0.058 -0.197 -5.097
5 O5' O O5* N N N 0 -0.444 0.725 -2.687
6 C5' C C5* N N N 0 0.561 -0.164 -2.199
7 C4' C C4* R N N 0 1.216 0.437 -0.955
8 O4' O O4* N N N 0 0.236 0.615 0.093
9 C3' C C3* S N N 0 2.255 -0.538 -0.359
10 O3' O O3* N N N 0 3.574 -0.183 -0.778
11 C1' C C1* R N N 0 0.997 0.702 1.318
12 C2' C C2* R N N 0 2.107 -0.361 1.168
13 O2' O O2* N N N 0 3.331 0.104 1.739
14 N1 N N1 N N N 0 0.148 0.394 2.471
15 C2 C C2 N N N 0 -0.524 -0.766 2.507
16 O2 O O2 N N N 0 -0.332 -1.59 1.633
17 N3 N N3 N N N 0 -1.397 -1.045 3.489
18 C4 C C4 N N N 0 -1.818 -0.085 4.333
19 O4 O O4 N N N 0 -2.546 -0.368 5.26
20 C5 C C5 N N N 0 -1.384 1.343 4.125
21 C6 C C6 N N N 0 0.04 1.36 3.566
22 HOP2 H 2HOP N N N 0 -2.593 0.534 -5.37
23 HOP3 H 3HOP N N N 0 0.415 0.674 -5.313
24 H5' H 1H5* N N N 0 1.317 -0.316 -2.97
25 H5'' H 2H5* N N N 0 0.106 -1.121 -1.943
26 H4' H H4* N N N 0 1.688 1.389 -1.198
27 H3' H H3* N N N 0 2.026 -1.563 -0.649
28 HO3' H *HO3 N N Y 0 4.18 -0.805 -0.353
29 H1' H H1* N N N 0 1.435 1.694 1.423
30 H2' H H2* N N N 0 1.803 -1.299 1.633
31 HO2' H *HO2 N N N 0 3.998 -0.572 1.562
32 HN3 H HN3 N N N 0 -1.731 -1.95 3.591
33 H51 H 1H5 N N N 0 -1.408 1.874 5.076
34 H52 H 2H5 N N N 0 -2.057 1.829 3.419
35 H61 H 1H6 N N N 0 0.743 1.094 4.356
36 H62 H 2H6 N N N 0 0.273 2.358 3.194



H2U : Chemical Bonds

Total Number of Bonds: 37
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 P OP1 P O doub 1.48 N N
2 P OP2 P O sing 1.61 N N
3 P OP3 P O sing 1.61 N N
4 P O5' P O sing 1.61 N N
5 OP2 HOP2 O H sing 0.97 N N
6 OP3 HOP3 O H sing 0.97 N N
7 O5' C5' O C sing 1.43 N N
8 C5' C4' C C sing 1.53 N N
9 C5' H5' C H sing 1.09 N N
10 C5' H5'' C H sing 1.09 N N
11 C4' O4' C O sing 1.45 N N
12 C4' C3' C C sing 1.54 N N
13 C4' H4' C H sing 1.09 N N
14 O4' C1' O C sing 1.44 N N
15 C3' O3' C O sing 1.43 N N
16 C3' C2' C C sing 1.54 N N
17 C3' H3' C H sing 1.09 N N
18 O3' HO3' O H sing 0.97 N N
19 C1' C2' C C sing 1.54 N N
20 C1' N1 C N sing 1.46 N N
21 C1' H1' C H sing 1.09 N N
22 C2' O2' C O sing 1.43 N N
23 C2' H2' C H sing 1.09 N N
24 O2' HO2' O H sing 0.97 N N
25 N1 C2 N C sing 1.34 N N
26 N1 C6 N C sing 1.46 N N
27 C2 O2 C O doub 1.22 N N
28 C2 N3 C N sing 1.34 N N
29 N3 C4 N C sing 1.35 N N
30 N3 HN3 N H sing 0.97 N N
31 C4 O4 C O doub 1.21 N N
32 C4 C5 C C sing 1.51 N N
33 C5 C6 C C sing 1.53 N N
34 C5 H51 C H sing 1.09 N N
35 C5 H52 C H sing 1.09 N N
36 C6 H61 C H sing 1.09 N N
37 C6 H62 C H sing 1.09 N N



H2U : Used in PDB Entries

Total Number of PDB Entries: 172
Ligand Code PDB Entry ID Type Total Distinct
H2U 1asy Open in New Window Polymer component 4 2
H2U 1asz Open in New Window Polymer component 4 2
H2U 1b23 Open in New Window Polymer component 2 2
H2U 1c0a Open in New Window Polymer component 3 3
H2U 1efw Open in New Window Polymer component 6 3
H2U 1eg0 Open in New Window Polymer component 1 1
H2U 1ehz Open in New Window Polymer component 2 2
H2U 1evv Open in New Window Polymer component 2 2
H2U 1f7u Open in New Window Polymer component 3 3
H2U 1f7v Open in New Window Polymer component 3 3
H2U 1fcw Open in New Window Polymer component 10 2
H2U 1fir Open in New Window Polymer component 3 3
H2U 1gsg Open in New Window Polymer component 1 1
H2U 1il2 Open in New Window Polymer component 4 2
H2U 1jgo Open in New Window Polymer component 6 4
H2U 1jgp Open in New Window Polymer component 6 4
H2U 1jgq Open in New Window Polymer component 6 4
H2U 1mj1 Open in New Window Polymer component 4 2
H2U 1ml5 Open in New Window Polymer component 2 2
H2U 1ob2 Open in New Window Polymer component 2 2
H2U 1ob5 Open in New Window Polymer component 6 2
H2U 1qf6 Open in New Window Polymer component 3 3
H2U 1ser Open in New Window Polymer component 1 1
H2U 1sz1 Open in New Window Polymer component 4 2
H2U 1tn1 Open in New Window Polymer component 2 2
H2U 1tn2 Open in New Window Polymer component 2 2
H2U 1tra Open in New Window Polymer component 2 2
H2U 1ttt Open in New Window Polymer component 6 2
H2U 1vtq Open in New Window Polymer component 2 2
H2U 1yfg Open in New Window Polymer component 2 2
H2U 2dlc Open in New Window Polymer component 1 1
H2U 2fmt Open in New Window Polymer component 2 1
H2U 2mn0 Open in New Window Polymer component 1 1
H2U 2om7 Open in New Window Polymer component 2 2
H2U 2tra Open in New Window Polymer component 2 2
H2U 2v0j Open in New Window Bound ligand 1 1
H2U 2z9q Open in New Window Polymer component 2 2
H2U 3b0u Open in New Window Polymer component 2 1
H2U 3b0v Open in New Window Polymer component 2 1
H2U 3bbv Open in New Window Polymer component 2 2
H2U 3cw5 Open in New Window Polymer component 1 1
H2U 3cw6 Open in New Window Polymer component 1 1
H2U 3deg Open in New Window Polymer component 2 2
H2U 3g1h Open in New Window Bound ligand 13 1
H2U 3j9y Open in New Window Polymer component 2 2
H2U 3jaq Open in New Window Polymer component 2 2
H2U 3jcj Open in New Window Polymer component 1 1
H2U 3jcn Open in New Window Polymer component 1 1
H2U 3jcs Open in New Window Polymer component 1 1
H2U 3kfu Open in New Window Polymer component 4 1
H2U 3tra Open in New Window Polymer component 2 2
H2U 3v11 Open in New Window Polymer component 1 1
H2U 486d Open in New Window Polymer component 6 6
H2U 4cxg Open in New Window Polymer component 2 2
H2U 4cxh Open in New Window Polymer component 2 2
H2U 4jyz Open in New Window Polymer component 1 1
H2U 4o8r Open in New Window Bound ligand 12 1
H2U 4tna Open in New Window Polymer component 2 2
H2U 4tra Open in New Window Polymer component 2 2
H2U 4v42 Open in New Window Polymer component 6 4
H2U 4v4i Open in New Window Polymer component 2 2
H2U 4v5g Open in New Window Polymer component 6 3
H2U 4v5l Open in New Window Polymer component 3 3
H2U 4v5p Open in New Window Polymer component 6 3
H2U 4v5q Open in New Window Polymer component 6 3
H2U 4v5r Open in New Window Polymer component 6 3
H2U 4v5s Open in New Window Polymer component 6 3
H2U 4v6k Open in New Window Polymer component 5 3
H2U 4v6l Open in New Window Polymer component 5 3
H2U 4v6n Open in New Window Polymer component 5 5
H2U 4v6o Open in New Window Polymer component 5 5
H2U 4v6p Open in New Window Polymer component 5 5
H2U 4v6q Open in New Window Polymer component 5 5
H2U 4v6r Open in New Window Polymer component 5 5
H2U 4v6s Open in New Window Polymer component 2 2
H2U 4v6v Open in New Window Polymer component 2 2
H2U 4v6y Open in New Window Polymer component 1 1
H2U 4v6z Open in New Window Polymer component 1 1
H2U 4v70 Open in New Window Polymer component 1 1
H2U 4v71 Open in New Window Polymer component 1 1
H2U 4v72 Open in New Window Polymer component 1 1
H2U 4v73 Open in New Window Polymer component 1 1
H2U 4v74 Open in New Window Polymer component 1 1
H2U 4v75 Open in New Window Polymer component 1 1
H2U 4v76 Open in New Window Polymer component 1 1
H2U 4v77 Open in New Window Polymer component 1 1
H2U 4v78 Open in New Window Polymer component 1 1
H2U 4v79 Open in New Window Polymer component 1 1
H2U 4v7h Open in New Window Polymer component 2 2
H2U 4wq1 Open in New Window Polymer component 2 1
H2U 4wr6 Open in New Window Polymer component 2 2
H2U 4wro Open in New Window Polymer component 9 4
H2U 4wsm Open in New Window Polymer component 2 1
H2U 4ybb Open in New Window Polymer component 1 1
H2U 5afi Open in New Window Polymer component 5 4
H2U 5ib8 Open in New Window Polymer component 1 1
H2U 5ibb Open in New Window Polymer component 1 1
H2U 5in3 Open in New Window Bound ligand 2 1
H2U 5iqr Open in New Window Polymer component 3 3
H2U 5it8 Open in New Window Polymer component 1 1
H2U 5j5b Open in New Window Polymer component 1 1
H2U 5j7l Open in New Window Polymer component 1 1
H2U 5j88 Open in New Window Polymer component 1 1
H2U 5j8a Open in New Window Polymer component 1 1
H2U 5j91 Open in New Window Polymer component 1 1
H2U 5jb3 Open in New Window Polymer component 1 1
H2U 5jbh Open in New Window Polymer component 1 1
H2U 5jc9 Open in New Window Polymer component 1 1
H2U 5ju8 Open in New Window Polymer component 3 3
H2U 5kcr Open in New Window Polymer component 1 1
H2U 5kcs Open in New Window Polymer component 3 3
H2U 5l3p Open in New Window Polymer component 5 5
H2U 5l4o Open in New Window Polymer component 1 1
H2U 5lza Open in New Window Polymer component 2 2
H2U 5lzb Open in New Window Polymer component 3 3
H2U 5lzc Open in New Window Polymer component 3 3
H2U 5lzd Open in New Window Polymer component 3 3
H2U 5lze Open in New Window Polymer component 3 3
H2U 5lzf Open in New Window Polymer component 3 3
H2U 5m1j Open in New Window Polymer component 2 2
H2U 5mdv Open in New Window Polymer component 1 1
H2U 5mdw Open in New Window Polymer component 1 1
H2U 5mdy Open in New Window Polymer component 1 1
H2U 5mdz Open in New Window Polymer component 1 1
H2U 5me0 Open in New Window Polymer component 1 1
H2U 5me1 Open in New Window Polymer component 1 1
H2U 5np6 Open in New Window Polymer component 1 1
H2U 5wdt Open in New Window Polymer component 5 4
H2U 5we4 Open in New Window Polymer component 5 4
H2U 5we6 Open in New Window Polymer component 5 4
H2U 5wf0 Open in New Window Polymer component 5 4
H2U 5wfk Open in New Window Polymer component 5 4
H2U 5wfs Open in New Window Polymer component 5 4
H2U 6fyx Open in New Window Polymer component 2 2
H2U 6fyy Open in New Window Polymer component 2 2
H2U 6gqd Open in New Window Bound ligand 1 1
H2U 6gsj Open in New Window Polymer component 6 3
H2U 6gsk Open in New Window Polymer component 6 3
H2U 6gsl Open in New Window Polymer component 2 1
H2U 6gsm Open in New Window Polymer component 2 2
H2U 6i7v Open in New Window Polymer component 1 1
H2U 6lvr Open in New Window Polymer component 4 2
H2U 6ore Open in New Window Polymer component 1 1
H2U 6orl Open in New Window Polymer component 1 1
H2U 6osk Open in New Window Polymer component 1 1
H2U 6osq Open in New Window Polymer component 1 1
H2U 6ost Open in New Window Polymer component 1 1
H2U 6ot3 Open in New Window Polymer component 1 1
H2U 6ouo Open in New Window Polymer component 1 1
H2U 6pj6 Open in New Window Polymer component 1 1
H2U 6qnq Open in New Window Polymer component 1 1
H2U 6qnr Open in New Window Polymer component 5 5
H2U 6sgc Open in New Window Polymer component 4 2
H2U 6sw9 Open in New Window Polymer component 1 1
H2U 6swc Open in New Window Polymer component 1 1
H2U 6tb3 Open in New Window Polymer component 2 2
H2U 6tna Open in New Window Polymer component 2 2
H2U 6u48 Open in New Window Polymer component 1 1
H2U 6v39 Open in New Window Polymer component 1 1
H2U 6v3a Open in New Window Polymer component 1 1
H2U 6xa1 Open in New Window Polymer component 2 2
H2U 6xz7 Open in New Window Polymer component 3 3
H2U 6ytf Open in New Window Polymer component 1 1
H2U 6ztj Open in New Window Polymer component 4 4
H2U 6ztl Open in New Window Polymer component 4 4
H2U 6ztm Open in New Window Polymer component 4 4
H2U 6ztn Open in New Window Polymer component 6 4
H2U 6zto Open in New Window Polymer component 4 4
H2U 6ztp Open in New Window Polymer component 4 4
H2U 6zu1 Open in New Window Polymer component 4 4
H2U 6zu9 Open in New Window Polymer component 2 2
H2U 7k00 Open in New Window Polymer component 1 1