Chemical Components in the PDB

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1U0 : Summary

Code

1U0

One-letter code

X

Molecule name

2-{4-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-[(1R)-1,2-dihydroxyethyl]-3-methylthiophen-2-yl}ethyl trihydrogen diphosphate

Systematic names

ProgramVersionName
ACDLabs 12.01 2-{4-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-[(1R)-1,2-dihydroxyethyl]-3-methylthiophen-2-yl}ethyl trihydrogen diphosphate
OpenEye OEToolkits 1.7.6 2-[4-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-5-[(1R)-1,2-bis(oxidanyl)ethyl]-3-methyl-thiophen-2-yl]ethyl phosphono hydrogen phosphate

Formula

C15 H23 N3 O9 P2 S

Formal charge

0

Molecular weight

483.37 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=P(O)(O)OP(=O)(O)OCCc1sc(c(c1C)Cc2cnc(nc2N)C)C(O)CO
SMILES CACTVS 3.370 Cc1ncc(Cc2c(C)c(CCO[P](O)(=O)O[P](O)(O)=O)sc2[CH](O)CO)c(N)n1
SMILES OpenEye OEToolkits 1.7.6 Cc1c(sc(c1Cc2cnc(nc2N)C)C(CO)O)CCOP(=O)(O)OP(=O)(O)O
Canonical SMILES CACTVS 3.370 Cc1ncc(Cc2c(C)c(CCO[P](O)(=O)O[P](O)(O)=O)sc2[C@H](O)CO)c(N)n1
Canonical SMILES OpenEye OEToolkits 1.7.6 Cc1c(sc(c1Cc2cnc(nc2N)C)[C@@H](CO)O)CCOP(=O)(O)OP(=O)(O)O

IUPAC InChI

InChI=1S/C15H23N3O9P2S/c1-8-11(5-10-6-17-9(2)18-15(10)16)14(12(20)7-19)30-13(8)3-4-26-29(24,25)27-28(21,22)23/h6,12,19-20H,3-5,7H2,1-2H3,(H,24,25)(H2,16,17,18)(H2,21,22,23)/t12-/m1/s1

IUPAC InChI key

AZNRIYLXMXTRTE-GFCCVEGCSA-N
1U0

wwPDB Information

Atom count

53 (30 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2013-06-05

Last modified at

2013-08-16

Status

Released

Obsoleted

Not Assigned



1U0 : 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 C2 C C2 N Y N 0 3.013 1.725 0.068
2 C2' C C2' N Y N 0 4.424 -3.455 0.947
3 C3 C C3 N Y N 0 2.868 0.811 -0.892
4 C4 C C4 N Y N 0 1.579 0.677 -1.38
5 C4' C C4' N Y N 0 5.229 -2.136 -0.756
6 C5 C C5 N Y N 0 0.678 1.48 -0.815
7 C5' C C5' N Y N 0 4.165 -1.254 -0.558
8 C6 C C6 N N N 0 -0.787 1.528 -1.168
9 C6' C C6' N Y N 0 3.246 -1.548 0.43
10 C7 C C7 N N N 0 -1.555 0.537 -0.291
11 C7' C C7' N N N 0 4.019 -0.016 -1.405
12 C8 C C8 R N N 0 4.309 2.061 0.759
13 C9 C C9 N N N 0 4.836 3.398 0.232
14 CM2 C CM2 N N N 0 4.563 -4.692 1.798
15 CM4 C CM4 N N N 0 1.223 -0.303 -2.468
16 H1 H H1 N N N 0 -8.941 0.764 -0.367
17 H10 H H10 N N N 0 0.217 -0.688 -2.296
18 H11 H H11 N N N 0 5.041 1.278 0.56
19 H12 H H12 N N N 0 3.446 2.838 2.418
20 H13 H H13 N N N 0 3.828 -0.304 -2.438
21 H14 H H14 N N N 0 4.937 0.569 -1.354
22 H15 H H15 N N N 0 2.408 -0.891 0.61
23 H16 H H16 N N N 0 4.036 -5.52 1.324
24 H17 H H17 N N N 0 5.618 -4.944 1.902
25 H18 H H18 N N N 0 4.135 -4.505 2.783
26 H19 H H19 N N N 0 6.96 -2.454 -1.809
27 H2 H H2 N N N 0 -7.46 -1.953 -0.99
28 H20 H H20 N N N 0 6.058 -1.142 -2.347
29 H21 H H21 N N N 0 4.921 3.352 -0.854
30 H22 H H22 N N N 0 4.147 4.195 0.509
31 H23 H H23 N N N 0 6.516 4.493 0.509
32 H3 H H3 N N N 0 -3.797 -2.095 -1.172
33 H4 H H4 N N N 0 -1.425 0.804 0.758
34 H5 H H5 N N N 0 -1.173 -0.47 -0.46
35 H6 H H6 N N N 0 -0.916 1.261 -2.217
36 H7 H H7 N N N 0 -1.169 2.535 -0.999
37 H8 H H8 N N N 0 1.259 0.199 -3.435
38 H9 H H9 N N N 0 1.934 -1.129 -2.461
39 N1' N N1' N Y N 0 3.406 -2.646 1.156
40 N3' N N3' N Y N 0 5.324 -3.214 0.015
41 N4' N N4' N N N 0 6.177 -1.885 -1.735
42 O10 O O10 N N N 0 6.121 3.66 0.8
43 O1A O O1A N N N 0 -3.982 -0.121 1.565
44 O1B O O1B N N N 0 -7.037 0.202 1.579
45 O2A O O2A N N N 0 -3.768 -1.883 -0.229
46 O2B O O2B N N N 0 -7.456 -1.665 -0.067
47 O3A O O3A N N N 0 -5.515 0.072 -0.431
48 O3B O O3B N N N 0 -8.021 0.834 -0.658
49 O7 O O7 N N N 0 -2.944 0.582 -0.625
50 O9 O O9 N N N 0 4.087 2.159 2.167
51 PA P PA N N N 0 -4.051 -0.333 0.102
52 PB P PB N N N 0 -7.008 -0.132 0.137
53 S1 S S1 N Y N 0 1.461 2.482 0.401



1U0 : Chemical Bonds

Total Number of Bonds: 54
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O1B PB O P doub 1.48 N N
2 O9 C8 O C sing 1.43 N N
3 O2B PB O P sing 1.61 N N
4 PB O3A P O sing 1.61 N N
5 PB O3B P O sing 1.61 N N
6 O3A PA O P sing 1.61 N N
7 C9 C8 C C sing 1.53 N N
8 C9 O10 C O sing 1.43 N N
9 N4' C4' N C sing 1.39 N N
10 C8 C2 C C sing 1.51 N N
11 O1A PA O P doub 1.48 N N
12 S1 C2 S C sing 1.76 N Y
13 S1 C5 S C sing 1.76 N Y
14 PA O2A P O sing 1.61 N N
15 PA O7 P O sing 1.61 N N
16 N3' C4' N C doub 1.33 N Y
17 N3' C2' N C sing 1.32 N Y
18 C2 C3 C C doub 1.33 N Y
19 C4' C5' C C sing 1.4 N Y
20 C7 O7 C O sing 1.43 N N
21 C7 C6 C C sing 1.53 N N
22 CM2 C2' C C sing 1.51 N N
23 C2' N1' C N doub 1.32 N Y
24 C5 C6 C C sing 1.51 N N
25 C5 C4 C C doub 1.33 N Y
26 C3 C7' C C sing 1.51 N N
27 C3 C4 C C sing 1.38 N Y
28 C5' C7' C C sing 1.51 N N
29 C5' C6' C C doub 1.38 N Y
30 C4 CM4 C C sing 1.51 N N
31 N1' C6' N C sing 1.33 N Y
32 O3B H1 O H sing 0.97 N N
33 O2B H2 O H sing 0.97 N N
34 O2A H3 O H sing 0.97 N N
35 C7 H4 C H sing 1.09 N N
36 C7 H5 C H sing 1.09 N N
37 C6 H6 C H sing 1.09 N N
38 C6 H7 C H sing 1.09 N N
39 CM4 H8 C H sing 1.09 N N
40 CM4 H9 C H sing 1.09 N N
41 CM4 H10 C H sing 1.09 N N
42 C8 H11 C H sing 1.09 N N
43 O9 H12 O H sing 0.97 N N
44 C7' H13 C H sing 1.09 N N
45 C7' H14 C H sing 1.09 N N
46 C6' H15 C H sing 1.08 N N
47 CM2 H16 C H sing 1.09 N N
48 CM2 H17 C H sing 1.09 N N
49 CM2 H18 C H sing 1.09 N N
50 N4' H19 N H sing 0.97 N N
51 N4' H20 N H sing 0.97 N N
52 C9 H21 C H sing 1.09 N N
53 C9 H22 C H sing 1.09 N N
54 O10 H23 O H sing 0.97 N N



1U0 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
1U0 4kxy Open in New Window Bound ligand 2 1