Chemical Components in the PDB

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56B : Summary

Code

56B

One-letter code

X

Molecule name

2-amino-5-({[(1S,4S,5R)-4,5-dihydroxycyclopent-2-en-1-yl]amino}methyl)-7-(5-O-phosphono-beta-D-ribofuranosyl)-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one

Systematic names

ProgramVersionName
ACDLabs 12.01 2-amino-5-({[(1S,4S,5R)-4,5-dihydroxycyclopent-2-en-1-yl]amino}methyl)-7-(5-O-phosphono-beta-D-ribofuranosyl)-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one
OpenEye OEToolkits 1.9.2 [(2R,3S,4R,5R)-5-[2-azanyl-5-[[[(1S,4S,5R)-4,5-bis(oxidanyl)cyclopent-2-en-1-yl]amino]methyl]-4-oxidanylidene-3H-pyrrolo[2,3-d]pyrimidin-7-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate

Formula

C17 H24 N5 O10 P

Formal charge

0

Molecular weight

489.374 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 n2(cc(CNC1C(O)C(O)C=C1)c3c2N=C(N)NC3=O)C4C(O)C(O)C(O4)COP(=O)(O)O
SMILES CACTVS 3.385 NC1=Nc2n(cc(CN[CH]3C=C[CH](O)[CH]3O)c2C(=O)N1)[CH]4O[CH](CO[P](O)(O)=O)[CH](O)[CH]4O
SMILES OpenEye OEToolkits 1.9.2 c1c(c2c(n1C3C(C(C(O3)COP(=O)(O)O)O)O)N=C(NC2=O)N)CNC4C=CC(C4O)O
Canonical SMILES CACTVS 3.385 NC1=Nc2n(cc(CN[C@H]3C=C[C@H](O)[C@@H]3O)c2C(=O)N1)[C@@H]4O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]4O
Canonical SMILES OpenEye OEToolkits 1.9.2 c1c(c2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N=C(NC2=O)N)CN[C@H]4C=C[C@@H]([C@@H]4O)O

IUPAC InChI

InChI=1S/C17H24N5O10P/c18-17-20-14-10(15(27)21-17)6(3-19-7-1-2-8(23)11(7)24)4-22(14)16-13(26)12(25)9(32-16)5-31-33(28,29)30/h1-2,4,7-9,11-13,16,19,23-26H,3,5H2,(H2,28,29,30)(H3,18,20,21,27)/t7-,8-,9+,11+,12+,13+,16+/m0/s1

IUPAC InChI key

BSABGNSIPKXNDL-AEZJAUAXSA-N
56B

wwPDB Information

Atom count

57 (33 without Hydrogen)

Polymer type

Ribonucleotide

Type description

RNA linking

Type code

ATOMN

Is modified

No

Standard parent

Not Assigned

Defined at

2015-08-03

Last modified at

2020-06-27

Status

Released

Obsoleted

Not Assigned



56B : Atoms of Molecule

Total Number of Atoms: 57
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N9 N N1 N Y N 0 0.257 1.569 0.022
2 C2' C C1 R N N 0 2.345 2.464 0.996
3 O2' O O1 N N N 0 2.504 3.854 0.709
4 P P P1 N N N 0 5.159 -2.961 -0.403
5 C1' C C2 R N N 0 1.696 1.735 -0.201
6 N10 N N2 N N N 0 -3.316 -1.045 0.01
7 O11 O O2 N N N 0 -3.763 -4.296 -0.24
8 C8 C C3 N Y N 0 -0.332 0.448 0.552
9 N3 N N3 N N N 0 -0.643 3.743 -0.78
10 O12 O O3 N N N 0 -6.277 -4.477 0.461
11 C7 C C4 N Y N 0 -1.661 0.627 0.62
12 N2 N N4 N N N 0 -1.633 5.707 -1.498
13 O6 O O4 N N N 0 -4.198 2.293 0.197
14 C9 C C5 N N N 0 -2.676 -0.359 1.14
15 N1 N N5 N N N 0 -2.97 3.969 -0.634
16 O4' O O5 N N N 0 2.349 0.448 -0.249
17 C10 C C6 S N N 0 -4.313 -2.016 0.48
18 O5' O O6 N N N 0 4.489 -1.505 -0.556
19 C11 C C7 R N N 0 -4.519 -3.13 -0.573
20 OP2 O O7 N N N 0 5.147 -3.71 -1.828
21 C12 C C8 S N N 0 -6.036 -3.397 -0.444
22 C13 C C9 N N N 0 -6.607 -2.111 0.108
23 C5 C C11 N Y N 0 -1.934 1.962 0.092
24 OP1 O O8 N N N 0 6.556 -2.815 0.065
25 C14 C C10 N N N 0 -5.667 -1.358 0.612
26 O3' O O9 N N N 0 4.778 2.727 0.963
27 C4 C C12 N Y N 0 -0.691 2.507 -0.262
28 C2 C C13 N N N 0 -1.736 4.448 -0.961
29 C6 C C14 N N N 0 -3.101 2.732 -0.104
30 C4' C C15 R N N 0 3.741 0.717 0.028
31 C5' C C16 N N N 0 4.444 -0.554 0.509
32 C3' C C17 S N N 0 3.723 1.782 1.152
33 H1 H H1 N N N 0 1.747 2.326 1.897
34 H2 H H2 N N N 0 2.934 4.355 1.416
35 H3 H H3 N N N 0 1.875 2.287 -1.124
36 H4 H H4 N N N 0 -3.73 -0.382 -0.628
37 H6 H H6 N N N 0 -3.86 -5.021 -0.872
38 H7 H H7 N N N 0 0.194 -0.441 0.866
39 H8 H H8 N N N 0 -7.214 -4.656 0.618
40 H9 H H9 N N N 0 -2.431 6.241 -1.638
41 H10 H H10 N N N 0 -0.763 6.063 -1.736
42 H14 H H14 N N N 0 -4.004 -2.446 1.433
43 H11 H H11 N N N 0 -3.432 0.17 1.72
44 H12 H H12 N N N 0 -2.178 -1.092 1.775
45 H13 H H13 N N N 0 -3.756 4.519 -0.779
46 H15 H H15 N N N 0 -4.267 -2.775 -1.572
47 H16 H H16 N N N 0 5.536 -4.595 -1.811
48 H17 H H17 N N N 0 -6.469 -3.616 -1.42
49 H18 H H18 N N N 0 -7.654 -1.849 0.088
50 H21 H H21 N N N 0 -5.835 -0.392 1.064
51 H23 H H23 N N N 0 4.813 3.417 1.639
52 H24 H H24 N N N 0 4.235 1.112 -0.859
53 H25 H H25 N N N 0 3.895 -0.976 1.351
54 H26 H H26 N N N 0 5.459 -0.311 0.823
55 H27 H H27 N N N 0 3.808 1.307 2.129
56 OP3 O O10 N N Y 0 4.324 -3.828 0.666
57 HOP3 H H5 N N Y 0 3.398 -3.964 0.424



56B : Chemical Bonds

Total Number of Bonds: 60
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N2 C2 N C sing 1.37 N N
2 C2 N1 C N sing 1.36 N N
3 C2 N3 C N doub 1.31 N N
4 N1 C6 N C sing 1.35 N N
5 N3 C4 N C sing 1.34 N N
6 C6 O6 C O doub 1.22 N N
7 C6 C5 C C sing 1.41 N N
8 C4 C5 C C doub 1.4 N Y
9 C4 N9 C N sing 1.36 N Y
10 C5 C7 C C sing 1.46 N Y
11 O4' C1' O C sing 1.44 N N
12 O4' C4' O C sing 1.44 N N
13 O3' C3' O C sing 1.43 N N
14 C1' N9 C N sing 1.47 N N
15 C1' C2' C C sing 1.54 N N
16 N9 C8 N C sing 1.37 N Y
17 C4' C3' C C sing 1.55 N N
18 C4' C5' C C sing 1.53 N N
19 C7 C8 C C doub 1.34 N Y
20 C7 C9 C C sing 1.51 N N
21 O2' C2' O C sing 1.43 N N
22 C3' C2' C C sing 1.55 N N
23 N10 C9 N C sing 1.47 N N
24 N10 C10 N C sing 1.47 N N
25 C12 C13 C C sing 1.51 N N
26 C12 O12 C O sing 1.43 N N
27 C12 C11 C C sing 1.55 N N
28 C13 C14 C C doub 1.31 N N
29 C14 C10 C C sing 1.51 N N
30 C5' O5' C O sing 1.43 N N
31 C10 C11 C C sing 1.55 N N
32 C11 O11 C O sing 1.43 N N
33 OP2 P O P sing 1.61 N N
34 O5' P O P sing 1.61 N N
35 P OP1 P O doub 1.48 N N
36 C2' H1 C H sing 1.09 N N
37 O2' H2 O H sing 0.97 N N
38 C1' H3 C H sing 1.09 N N
39 N10 H4 N H sing 1.01 N N
40 O11 H6 O H sing 0.97 N N
41 C8 H7 C H sing 1.08 N N
42 O12 H8 O H sing 0.97 N N
43 N2 H9 N H sing 0.97 N N
44 N2 H10 N H sing 0.97 N N
45 C9 H11 C H sing 1.09 N N
46 C9 H12 C H sing 1.09 N N
47 N1 H13 N H sing 0.97 N N
48 C10 H14 C H sing 1.09 N N
49 C11 H15 C H sing 1.09 N N
50 OP2 H16 O H sing 0.97 N N
51 C12 H17 C H sing 1.09 N N
52 C13 H18 C H sing 1.08 N N
53 C14 H21 C H sing 1.08 N N
54 O3' H23 O H sing 0.97 N N
55 C4' H24 C H sing 1.09 N N
56 C5' H25 C H sing 1.09 N N
57 C5' H26 C H sing 1.09 N N
58 C3' H27 C H sing 1.09 N N
59 P OP3 P O sing 1.61 N N
60 OP3 HOP3 O H sing 0.97 N N



56B : Used in PDB Entries

Total Number of PDB Entries: 12
Ligand Code PDB Entry ID Type Total Distinct
56B 5d0b Open in New Window Polymer component 1 1
56B 7u91 Open in New Window Bound ligand 2 1
56B 7ulc Open in New Window Bound ligand 2 1
56B 7y7d Open in New Window Polymer component 1 1
56B 7y7e Open in New Window Polymer component 1 1
56B 7y7f Open in New Window Polymer component 1 1
56B 7y7g Open in New Window Polymer component 1 1
56B 7y7h Open in New Window Polymer component 1 1
56B 8jdj Open in New Window Polymer component 2 1
56B 8jdk Open in New Window Polymer component 2 1
56B 8jdl Open in New Window Polymer component 1 1
56B 8jdm Open in New Window Polymer component 2 1