Chemical Components in the PDB

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P0C : Summary

Code

P0C

One-letter code

X

Molecule name

6-methyl-3-(beta-D-ribofuranosyl)-3,7-dihydro-2H-pyrrolo[2,3-d]pyrimidin-2-one

Systematic names

ProgramVersionName
ACDLabs 12.01 6-methyl-3-(beta-D-ribofuranosyl)-3,7-dihydro-2H-pyrrolo[2,3-d]pyrimidin-2-one
OpenEye OEToolkits 1.9.2 3-[(2R,3R,4S,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-6-methyl-7H-pyrrolo[2,3-d]pyrimidin-2-one

Formula

C12 H15 N3 O5

Formal charge

0

Molecular weight

281.265 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C1N=C3C(=CN1C2OC(C(O)C2O)CO)C=C(N3)C
SMILES CACTVS 3.385 CC1=CC2=CN([CH]3O[CH](CO)[CH](O)[CH]3O)C(=O)N=C2N1
SMILES OpenEye OEToolkits 1.9.2 CC1=CC2=CN(C(=O)N=C2N1)C3C(C(C(O3)CO)O)O
Canonical SMILES CACTVS 3.385 CC1=CC2=CN([C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O)C(=O)N=C2N1
Canonical SMILES OpenEye OEToolkits 1.9.2 CC1=CC2=CN(C(=O)N=C2N1)[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O

IUPAC InChI

InChI=1S/C12H15N3O5/c1-5-2-6-3-15(12(19)14-10(6)13-5)11-9(18)8(17)7(4-16)20-11/h2-3,7-9,11,16-18H,4H2,1H3,(H,13,14,19)/t7-,8-,9-,11-/m1/s1

IUPAC InChI key

GCNYJWODKQPZDE-TURQNECASA-N
P0C

wwPDB Information

Atom count

35 (20 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2014-05-16

Last modified at

2021-03-13

Status

Released

Obsoleted

Not Assigned



P0C : Atoms of Molecule

Total Number of Atoms: 35
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C14 C C1 N N N 0 -2.586 0.353 -0.551
2 C16 C C2 N N N 0 -4.804 0.023 -0.319
3 C17 C C3 N N N 0 -6.3 0.086 -0.489
4 O01 O O1 N N N 0 3.915 2.03 -0.201
5 C02 C C4 S N N 0 3.3 0.892 0.407
6 C03 C C5 R N N 0 3.272 -0.295 -0.576
7 C04 C C6 N N N 0 4.051 -1.474 0.01
8 O05 O O2 N N N 0 4.118 -2.527 -0.954
9 O06 O O3 N N N 0 1.895 -0.663 -0.762
10 C07 C C7 R N N 0 1.105 0.52 -0.515
11 C08 C C8 R N N 0 1.807 1.175 0.702
12 O09 O O4 N N N 0 1.553 2.581 0.741
13 N10 N N1 N N N 0 -0.276 0.159 -0.185
14 C11 C C9 N N N 0 -0.517 -0.715 0.808
15 N12 N N2 N N N 0 -1.752 -1.08 1.14
16 C13 C C10 N N N 0 -2.801 -0.579 0.5
17 C15 C C11 N N N 0 -3.919 0.713 -1.049
18 N18 N N3 N N N 0 -4.149 -0.752 0.609
19 C19 C C12 N N N 0 -1.297 0.708 -0.881
20 O20 O O5 N N N 0 0.426 -1.195 1.417
21 H1 H H1 N N N 0 -6.617 -0.671 -1.206
22 H2 H H2 N N N 0 -6.783 -0.097 0.47
23 H3 H H3 N N N 0 -6.583 1.074 -0.855
24 H4 H H4 N N N 0 4.835 1.888 -0.461
25 H5 H H5 N N N 0 3.827 0.618 1.321
26 H6 H H6 N N N 0 3.711 0.002 -1.529
27 H7 H H7 N N N 0 5.06 -1.152 0.267
28 H8 H H8 N N N 0 3.546 -1.834 0.906
29 H9 H H9 N N N 0 4.599 -3.309 -0.65
30 H10 H H10 N N N 0 1.131 1.186 -1.377
31 H11 H H11 N N N 0 1.498 0.699 1.633
32 H12 H H12 N N N 0 1.972 3.036 1.485
33 H14 H H14 N N N 0 -4.143 1.402 -1.85
34 H15 H H15 N N N 0 -4.584 -1.337 1.25
35 H16 H H16 N N N 0 -1.105 1.411 -1.679



P0C : 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 O20 C11 O C doub 1.22 N N
2 C11 N12 C N sing 1.33 N N
3 C11 N10 C N sing 1.34 N N
4 N12 C13 N C doub 1.33 N N
5 O09 C08 O C sing 1.43 N N
6 C08 C07 C C sing 1.55 N N
7 C08 C02 C C sing 1.55 N N
8 C13 N18 C N sing 1.36 N N
9 C13 C14 C C sing 1.42 N N
10 N10 C07 N C sing 1.47 N N
11 N10 C19 N C sing 1.35 N N
12 C07 O06 C O sing 1.44 N N
13 N18 C16 N C sing 1.38 N N
14 O06 C03 O C sing 1.44 N N
15 C19 C14 C C doub 1.38 N N
16 C14 C15 C C sing 1.47 N N
17 C02 O01 C O sing 1.43 N N
18 C02 C03 C C sing 1.54 N N
19 C16 C15 C C doub 1.34 N N
20 C16 C17 C C sing 1.51 N N
21 C03 C04 C C sing 1.53 N N
22 C04 O05 C O sing 1.43 N N
23 C17 H1 C H sing 1.09 N N
24 C17 H2 C H sing 1.09 N N
25 C17 H3 C H sing 1.09 N N
26 O01 H4 O H sing 0.97 N N
27 C02 H5 C H sing 1.09 N N
28 C03 H6 C H sing 1.09 N N
29 C04 H7 C H sing 1.09 N N
30 C04 H8 C H sing 1.09 N N
31 O05 H9 O H sing 0.97 N N
32 C07 H10 C H sing 1.09 N N
33 C08 H11 C H sing 1.09 N N
34 O09 H12 O H sing 0.97 N N
35 C15 H14 C H sing 1.08 N N
36 N18 H15 N H sing 0.97 N N
37 C19 H16 C H sing 1.08 N N



P0C : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
P0C 4pd8 Open in New Window Bound ligand 1 1