Chemical Components in the PDB

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JMH : Summary

Code

JMH

One-letter code

C

Molecule name

3-Methylcytidine- 5'-monophosphate

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 [(2~{R},3~{S},4~{R},5~{R})-5-(4-azanylidene-3-methyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate

Formula

C10 H16 N3 O8 P

Formal charge

0

Molecular weight

337.223 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CN1C(=N)C=CN([CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O)C1=O
SMILES OpenEye OEToolkits 2.0.7 CN1C(=N)C=CN(C1=O)C2C(C(C(O2)COP(=O)(O)O)O)O
Canonical SMILES CACTVS 3.385 CN1C(=N)C=CN([C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O)C1=O
Canonical SMILES OpenEye OEToolkits 2.0.7 [H]/N=C\1/C=CN(C(=O)N1C)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O

IUPAC InChI

InChI=1S/C10H16N3O8P/c1-12-6(11)2-3-13(10(12)16)9-8(15)7(14)5(21-9)4-20-22(17,18)19/h2-3,5,7-9,11,14-15H,4H2,1H3,(H2,17,18,19)/b11-6-/t5-,7-,8-,9-/m1/s1

IUPAC InChI key

ZEGVEFNYAXGPPR-MJSKEWNISA-N
JMH

wwPDB Information

Atom count

38 (22 without Hydrogen)

Polymer type

Ribonucleotide

Type description

RNA linking

Type code

ATOMN

Is modified

Yes

Standard parent

C

Defined at

2019-03-12

Last modified at

2019-04-19

Status

Released

Obsoleted

Not Assigned



JMH : Atoms of Molecule

Total Number of Atoms: 38
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N1 N N1 N N N 0 -2.083 0.035 0.009
2 C2 C C1 N N N 0 -3.232 0.032 0.702
3 C5 C C2 N N N 0 -2.786 1.847 -1.32
4 C1' C C3 R N N 0 -1.051 -0.953 0.335
5 C2' C C4 R N N 0 -0.83 -1.923 -0.853
6 C3' C C5 S N N 0 0.619 -2.411 -0.608
7 C4 C C6 N N N 0 -4.043 1.857 -0.56
8 C4' C C7 R N N 0 1.234 -1.328 0.299
9 C5' C C8 N N N 0 2.468 -0.725 -0.374
10 C6 C C9 N N N 0 -1.85 0.934 -1.001
11 C31 C C10 N N N 0 -5.452 0.891 1.226
12 N3 N N2 N N N 0 -4.214 0.917 0.444
13 N4 N N3 N N N 0 -4.984 2.725 -0.832
14 O2 O O1 N N N 0 -3.391 -0.789 1.585
15 O2' O O2 N N N 0 -1.752 -3.014 -0.799
16 O3' O O3 N N N 0 0.614 -3.677 0.056
17 O4' O O4 N N N 0 0.234 -0.313 0.491
18 O5' O O5 N N N 0 3.099 0.193 0.521
19 OP1 O O6 N N N 0 5.49 0.069 -0.277
20 OP2 O O7 N N N 0 4.109 2.029 -1.067
21 P P P1 N N N 0 4.43 1.014 0.141
22 OP3 O O8 N N Y 0 4.931 1.848 1.424
23 H1 H H1 N N N 0 -2.614 2.562 -2.111
24 H2 H H2 N N N 0 -1.32 -1.504 1.236
25 H3 H H3 N N N 0 -0.908 -1.398 -1.805
26 H4 H H4 N N N 0 1.164 -2.478 -1.549
27 H6 H H6 N N N 0 1.51 -1.762 1.26
28 H7 H H7 N N N 0 3.168 -1.521 -0.629
29 H8 H H8 N N N 0 2.168 -0.201 -1.281
30 H9 H H9 N N N 0 -0.915 0.91 -1.54
31 H10 H H10 N N N 0 -6.287 0.631 0.576
32 H11 H H11 N N N 0 -5.365 0.149 2.02
33 H12 H H12 N N N 0 -5.625 1.874 1.665
34 H13 H H13 N N N 0 -5.838 2.674 -0.375
35 H16 H H16 N N N 0 -1.653 -3.649 -1.522
36 H17 H H17 N N N 0 0.186 -4.383 -0.446
37 H18 H H18 N N N 0 3.422 2.678 -0.862
38 H19 H H19 N N N 0 5.732 2.368 1.268



JMH : Chemical Bonds

Total Number of Bonds: 39
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 OP1 P O P doub 1.48 N N
2 N4 C4 N C doub 1.31 N N
3 P OP2 P O sing 1.61 N N
4 P O5' P O sing 1.61 N N
5 C5 C4 C C sing 1.47 N N
6 C5 C6 C C doub 1.35 N N
7 C4 N3 C N sing 1.39 N N
8 C6 N1 C N sing 1.37 N N
9 O4' C1' O C sing 1.44 N N
10 O4' C4' O C sing 1.44 N N
11 N3 C31 N C sing 1.46 N N
12 N3 C2 N C sing 1.35 N N
13 O5' C5' O C sing 1.43 N N
14 C5' C4' C C sing 1.53 N N
15 N1 C2 N C sing 1.34 N N
16 N1 C1' N C sing 1.47 N N
17 C2 O2 C O doub 1.22 N N
18 C1' C2' C C sing 1.55 N N
19 C4' C3' C C sing 1.54 N N
20 C3' C2' C C sing 1.55 N N
21 C3' O3' C O sing 1.43 N N
22 C2' O2' C O sing 1.43 N N
23 P OP3 P O sing 1.61 N N
24 C5 H1 C H sing 1.08 N N
25 C1' H2 C H sing 1.09 N N
26 C2' H3 C H sing 1.09 N N
27 C3' H4 C H sing 1.09 N N
28 C4' H6 C H sing 1.09 N N
29 C5' H7 C H sing 1.09 N N
30 C5' H8 C H sing 1.09 N N
31 C6 H9 C H sing 1.08 N N
32 C31 H10 C H sing 1.09 N N
33 C31 H11 C H sing 1.09 N N
34 C31 H12 C H sing 1.09 N N
35 N4 H13 N H sing 0.97 N N
36 O2' H16 O H sing 0.97 N N
37 O3' H17 O H sing 0.97 N N
38 OP2 H18 O H sing 0.97 N N
39 OP3 H19 O H sing 0.97 N N



JMH : Used in PDB Entries

Total Number of PDB Entries: 21
Ligand Code PDB Entry ID Type Total Distinct
JMH 6qzp Open in New Window Polymer component 2 2
JMH 6ybs Open in New Window Polymer component 1 1
JMH 6ybw Open in New Window Polymer component 1 1
JMH 6zj3 Open in New Window Polymer component 1 1
JMH 6zmw Open in New Window Polymer component 1 1
JMH 7f5s Open in New Window Polymer component 1 1
JMH 7xnx Open in New Window Polymer component 2 2
JMH 7xny Open in New Window Polymer component 2 2
JMH 8oz0 Open in New Window Polymer component 1 1
JMH 8p7b Open in New Window Polymer component 1 1
JMH 8p7c Open in New Window Polymer component 2 1
JMH 8p7d Open in New Window Polymer component 1 1
JMH 8pj1 Open in New Window Polymer component 1 1
JMH 8pj2 Open in New Window Polymer component 1 1
JMH 8pj3 Open in New Window Polymer component 1 1
JMH 8pj4 Open in New Window Polymer component 1 1
JMH 8pj5 Open in New Window Polymer component 1 1
JMH 8pj6 Open in New Window Polymer component 1 1
JMH 8rg0 Open in New Window Polymer component 1 1
JMH 9bkd Open in New Window Polymer component 1 1
JMH 9bln Open in New Window Polymer component 1 1