Chemical Components in the PDB

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5HU : Summary

Code

5HU

One-letter code

U

Molecule name

5-HYDROXYMETHYLURIDINE-2'-DEOXY-5'-MONOPHOSPHATE

Systematic names

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

Formula

C10 H15 N2 O9 P

Formal charge

0

Molecular weight

338.208 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C1NC(=O)N(C=C1CO)C2OC(C(O)C2)COP(=O)(O)O
SMILES CACTVS 3.341 OCC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O
SMILES OpenEye OEToolkits 1.5.0 C1C(C(OC1N2C=C(C(=O)NC2=O)CO)COP(=O)(O)O)O
Canonical SMILES CACTVS 3.341 OCC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O
Canonical SMILES OpenEye OEToolkits 1.5.0 C1[C@@H]([C@H](O[C@H]1N2C=C(C(=O)NC2=O)CO)COP(=O)(O)O)O

IUPAC InChI

InChI=1S/C10H15N2O9P/c13-3-5-2-12(10(16)11-9(5)15)8-1-6(14)7(21-8)4-20-22(17,18)19/h2,6-8,13-14H,1,3-4H2,(H,11,15,16)(H2,17,18,19)/t6-,7+,8+/m0/s1

IUPAC InChI key

WEBVWKFGRVLCNS-XLPZGREQSA-N
5HU

wwPDB Information

Atom count

37 (22 without Hydrogen)

Polymer type

Deoxy ribonucleotide

Type description

DNA LINKING

Type code

ATOMN

Is modified

Yes

Standard parent

DU

Defined at

2002-09-26

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



5HU : Atoms of Molecule

Total Number of Atoms: 37
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 -4.427 1.005 -0.232
2 OP1 O O1P N N N 0 -3.996 1.758 0.967
3 OP2 O O2P N N N 0 -5.062 2.024 -1.306
4 OP3 O O3P N N Y 0 -5.53 -0.089 0.188
5 O5' O O5* N N N 0 -3.156 0.262 -0.884
6 C5' C C5* N N N 0 -2.568 -0.533 0.147
7 C4' C C4* R N N 0 -1.348 -1.27 -0.409
8 O4' O O4* N N N 0 -0.264 -0.348 -0.662
9 C3' C C3* S N N 0 -0.764 -2.237 0.651
10 O3' O O3* N N N 0 -1.428 -3.502 0.61
11 C2' C C2* N N N 0 0.708 -2.371 0.193
12 C1' C C1* R N N 0 0.947 -1.123 -0.679
13 N1 N N1 N N N 0 2.051 -0.334 -0.128
14 C2 C C2 N N N 0 1.923 0.237 1.083
15 O2 O O2 N N N 0 0.89 0.09 1.708
16 N3 N N3 N N N 0 2.922 0.966 1.614
17 C4 C C4 N N N 0 4.075 1.134 0.936
18 O4 O O4 N N N 0 4.979 1.794 1.415
19 C5 C C5 N N N 0 4.222 0.543 -0.342
20 C5A C C5A N N N 0 5.499 0.718 -1.123
21 C6 C C6 N N N 0 3.204 -0.184 -0.851
22 O5B O O5B N N N 0 5.395 0.024 -2.368
23 HO2P H HO2P N N N 0 -5.818 2.446 -0.876
24 HO3P H HO3P N N N 0 -5.783 -0.555 -0.62
25 H5' H 1H5* N N N 0 -3.298 -1.258 0.507
26 H5'' H 2H5* N N N 0 -2.26 0.11 0.971
27 HC4' H HC4* N N N 0 -1.61 -1.811 -1.319
28 HC3' H HC3* N N N 0 -0.823 -1.802 1.649
29 HO3' H HO3* N N Y 0 -0.96 -4.084 1.224
30 H2' H 1H2* N N N 0 0.844 -3.279 -0.395
31 H2'' H 2H2* N N N 0 1.378 -2.369 1.053
32 HC1' H HC1* N N N 0 1.18 -1.424 -1.701
33 HN3 H HN3 N N N 0 2.813 1.371 2.489
34 H5A1 H 1H5A N N N 0 6.333 0.314 -0.55
35 H5A2 H 2H5A N N N 0 5.667 1.779 -1.311
36 HC6 H HC6 N N N 0 3.299 -0.645 -1.822
37 HO5B H HO5B N N N 0 6.231 0.162 -2.835



5HU : Chemical Bonds

Total Number of Bonds: 38
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 HO2P O H sing 0.97 N N
6 OP3 HO3P 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 1.55 N N
13 C4' HC4' 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 1.55 N N
17 C3' HC3' C H sing 1.09 N N
18 O3' HO3' O H sing 0.97 N N
19 C2' C1' C C sing 1.54 N N
20 C2' H2' C H sing 1.09 N N
21 C2' H2'' C H sing 1.09 N N
22 C1' N1 C N sing 1.46 N N
23 C1' HC1' C H sing 1.09 N N
24 N1 C2 N C sing 1.34 N N
25 N1 C6 N C sing 1.37 N N
26 C2 O2 C O doub 1.22 N N
27 C2 N3 C N sing 1.35 N N
28 N3 C4 N C sing 1.35 N N
29 N3 HN3 N H sing 0.97 N N
30 C4 O4 C O doub 1.22 N N
31 C4 C5 C C sing 1.42 N N
32 C5 C5A C C sing 1.51 N N
33 C5 C6 C C doub 1.35 N N
34 C5A O5B C O sing 1.43 N N
35 C5A H5A1 C H sing 1.09 N N
36 C5A H5A2 C H sing 1.09 N N
37 C6 HC6 C H sing 1.08 N N
38 O5B HO5B O H sing 0.97 N N



5HU : Used in PDB Entries

Total Number of PDB Entries: 9
Ligand Code PDB Entry ID Type Total Distinct
5HU 1mrs Open in New Window Bound ligand 1 1
5HU 1y6g Open in New Window Polymer component 1 1
5HU 1y8z Open in New Window Polymer component 1 1
5HU 4e9h Open in New Window Polymer component 1 1
5HU 4ea4 Open in New Window Polymer component 1 1
5HU 4ea5 Open in New Window Polymer component 1 1
5HU 4ew0 Open in New Window Polymer component 1 1
5HU 7jxf Open in New Window Bound ligand 1 1
5HU 8qhq Open in New Window Bound ligand 6 1