Chemical Components in the PDB

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4AC : Summary

Code

4AC

One-letter code

N

Molecule name

N(4)-ACETYLCYTIDINE-5'-MONOPHOSPHATE

Systematic names

ProgramVersionName
ACDLabs 10.04 N-acetylcytidine 5'-(dihydrogen phosphate)
OpenEye OEToolkits 1.5.0 [(2R,3S,4R,5R)-5-(4-acetamido-2-oxo-pyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl dihydrogen phosphate

Formula

C11 H16 N3 O9 P

Formal charge

0

Molecular weight

365.233 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(NC1=NC(=O)N(C=C1)C2OC(C(O)C2O)COP(=O)(O)O)C
SMILES CACTVS 3.341 CC(=O)NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O
SMILES OpenEye OEToolkits 1.5.0 CC(=O)NC1=NC(=O)N(C=C1)C2C(C(C(O2)COP(=O)(O)O)O)O
Canonical SMILES CACTVS 3.341 CC(=O)NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O
Canonical SMILES OpenEye OEToolkits 1.5.0 CC(=O)NC1=NC(=O)N(C=C1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O

IUPAC InChI

InChI=1S/C11H16N3O9P/c1-5(15)12-7-2-3-14(11(18)13-7)10-9(17)8(16)6(23-10)4-22-24(19,20)21/h2-3,6,8-10,16-17H,4H2,1H3,(H2,19,20,21)(H,12,13,15,18)/t6-,8-,9-,10-/m1/s1

IUPAC InChI key

ZVZPSHDOUJPFEV-PEBGCTIMSA-N
4AC

wwPDB Information

Atom count

40 (24 without Hydrogen)

Polymer type

Ribonucleotide

Type description

RNA LINKING

Type code

ATOMN

Is modified

Yes

Standard parent

Not Assigned

Defined at

2001-01-18

Last modified at

2024-09-27

Status

Released

Obsoleted

Not Assigned



4AC : Atoms of Molecule

Total Number of Atoms: 40
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 OP3 O O3P N N Y 0 1.198 0.588 -4.548
2 P P P N N N 0 2.787 0.324 -4.407
3 OP1 O O1P N N N 0 3.659 1.172 -5.286
4 OP2 O O2P N N N 0 2.921 -1.27 -4.647
5 O5' O O5* N N N 0 3.063 0.476 -2.819
6 C5' C C5* N N N 0 2.282 -0.292 -1.921
7 C4' C C4* R N N 0 2.725 0.023 -0.498
8 O4' O O4* N N N 0 2.47 1.422 -0.246
9 C3' C C3* S N N 0 1.94 -0.742 0.56
10 O3' O O3* N N N 0 2.742 -0.809 1.739
11 C2' C C2* R N N 0 0.748 0.163 0.786
12 O2' O O2* N N N 0 0.137 -0.058 2.041
13 C1' C C1* R N N 0 1.373 1.543 0.675
14 N1 N N1 N N N 0 0.452 2.524 0.177
15 C2 C C2 N N N 0 -0.31 3.348 1.043
16 O2 O O2 N N N 0 -0.205 3.248 2.267
17 N3 N N3 N N N 0 -1.18 4.274 0.492
18 C4 C C4 N N N 0 -1.304 4.394 -0.804
19 N4 N N4 N N N 0 -2.152 5.297 -1.374
20 C5 C C5 N N N 0 -0.524 3.549 -1.744
21 C6 C C6 N N N 0 0.307 2.665 -1.195
22 C7 C C7 N N N 0 -2.955 6.163 -0.648
23 O7 O O7 N N N 0 -3.014 6.239 0.578
24 CM7 C CM7 N N N 0 -3.816 7.025 -1.532
25 H5'' H 2H5* N N N 0 2.428 -1.352 -2.133
26 HOP3 H 3HOP N N N 0 0.799 0.616 -5.443
27 HOP2 H 2HOP N N N 0 2.886 -1.617 -5.563
28 H5' H 1H5* N N N 0 1.229 -0.035 -2.051
29 H4' H H4* N N N 0 3.804 -0.139 -0.41
30 H3' H H3* N N N 0 1.675 -1.764 0.277
31 HO3' H H3T N N Y 0 3.447 -0.153 1.628
32 H2' H H2* N N N 0 0.0 0.004 0.0
33 HO2' H 2HO* N N N 0 -0.494 0.669 2.185
34 H1' H H1* N N N 0 1.754 1.91 1.633
35 H4 H H4 N N N 0 -2.199 5.337 -2.389
36 H5 H H5 N N N 0 -0.639 3.662 -2.814
37 H6 H H6 N N N 0 0.914 2.009 -1.808
38 HM73 H 3HM7 N N N 0 -3.29 7.294 -2.453
39 HM71 H 1HM7 N N N 0 -4.076 7.946 -1.003
40 HM72 H 2HM7 N N N 0 -4.731 6.481 -1.784



4AC : Chemical Bonds

Total Number of Bonds: 41
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 OP3 P O P sing 1.62 N N
2 OP3 HOP3 O H sing 0.98 N N
3 P OP1 P O doub 1.5 N N
4 P OP2 P O sing 1.62 N N
5 P O5' P O sing 1.62 N N
6 OP2 HOP2 O H sing 0.98 N N
7 O5' C5' O C sing 1.42 N N
8 C5' C4' C C sing 1.52 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 1.44 N N
12 C4' C3' C C sing 1.52 N N
13 C4' H4' 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 1.51 N N
17 C3' H3' C H sing 1.09 N N
18 O3' HO3' O H sing 0.97 N N
19 C2' O2' C O sing 1.41 N N
20 C2' C1' C C sing 1.52 N N
21 C2' H2' C H sing 1.1 N N
22 O2' HO2' O H sing 0.97 N N
23 C1' N1 C N sing 1.43 N N
24 C1' H1' C H sing 1.09 N N
25 N1 C2 N C sing 1.42 N N
26 N1 C6 N C sing 1.39 N N
27 C2 O2 C O doub 1.23 N N
28 C2 N3 C N sing 1.38 N N
29 N3 C4 N C doub 1.31 N N
30 C4 N4 C N sing 1.36 N N
31 C4 C5 C C sing 1.49 N N
32 N4 C7 N C sing 1.39 N N
33 N4 H4 N H sing 1.02 N N
34 C5 C6 C C doub 1.33 N N
35 C5 H5 C H sing 1.08 N N
36 C6 H6 C H sing 1.08 N N
37 C7 O7 C O doub 1.23 N N
38 C7 CM7 C C sing 1.51 N N
39 CM7 HM71 C H sing 1.09 N N
40 CM7 HM72 C H sing 1.09 N N
41 CM7 HM73 C H sing 1.09 N N



4AC : Used in PDB Entries

Total Number of PDB Entries: 98
Ligand Code PDB Entry ID Type Total Distinct
4AC 6mtb Open in New Window Polymer component 2 2
4AC 6mtc Open in New Window Polymer component 2 2
4AC 6mtd Open in New Window Polymer component 1 1
4AC 6mte Open in New Window Polymer component 2 2
4AC 6ole Open in New Window Polymer component 2 2
4AC 6olf Open in New Window Polymer component 2 2
4AC 6oli Open in New Window Polymer component 2 2
4AC 6om0 Open in New Window Polymer component 2 2
4AC 6om7 Open in New Window Polymer component 2 2
4AC 6qzp Open in New Window Polymer component 2 2
4AC 6skf Open in New Window Polymer component 63 63
4AC 6sw9 Open in New Window Polymer component 32 32
4AC 6swc Open in New Window Polymer component 32 32
4AC 6swd Open in New Window Polymer component 24 24
4AC 6swe Open in New Window Polymer component 7 7
4AC 6th6 Open in New Window Polymer component 4 4
4AC 6xa1 Open in New Window Polymer component 2 2
4AC 6zxg Open in New Window Polymer component 2 2
4AC 6zxh Open in New Window Polymer component 2 2
4AC 7ls1 Open in New Window Polymer component 1 1
4AC 7ls2 Open in New Window Polymer component 1 1
4AC 7mpi Open in New Window Polymer component 2 2
4AC 7mpj Open in New Window Polymer component 2 2
4AC 7mqa Open in New Window Polymer component 1 1
4AC 7n8b Open in New Window Polymer component 2 2
4AC 7o7y Open in New Window Polymer component 2 2
4AC 7o7z Open in New Window Polymer component 2 2
4AC 7o80 Open in New Window Polymer component 2 2
4AC 7o81 Open in New Window Polymer component 2 2
4AC 7oyd Open in New Window Polymer component 2 2
4AC 7pwf Open in New Window Polymer component 1 1
4AC 7pwo Open in New Window Polymer component 1 1
4AC 7q4k Open in New Window Polymer component 1 1
4AC 7qgg Open in New Window Polymer component 2 2
4AC 7qix Open in New Window Polymer component 1 1
4AC 7qiy Open in New Window Polymer component 1 1
4AC 7qiz Open in New Window Polymer component 2 2
4AC 7r4x Open in New Window Polymer component 2 2
4AC 7ucj Open in New Window Polymer component 2 2
4AC 7uck Open in New Window Polymer component 3 3
4AC 7vnv Open in New Window Polymer component 2 1
4AC 7vnw Open in New Window Polymer component 2 1
4AC 7xnx Open in New Window Polymer component 2 2
4AC 7xny Open in New Window Polymer component 2 2
4AC 7zag Open in New Window Polymer component 29 29
4AC 7zah Open in New Window Polymer component 29 29
4AC 7zai Open in New Window Polymer component 29 29
4AC 7zhg Open in New Window Polymer component 29 29
4AC 7zjw Open in New Window Polymer component 2 2
4AC 7zjx Open in New Window Polymer component 2 2
4AC 8auv Open in New Window Polymer component 2 2
4AC 8b2l Open in New Window Polymer component 2 2
4AC 8btk Open in New Window Polymer component 2 2
4AC 8ccs Open in New Window Polymer component 2 2
4AC 8cdl Open in New Window Polymer component 2 2
4AC 8cdr Open in New Window Polymer component 2 2
4AC 8ceh Open in New Window Polymer component 2 2
4AC 8cf5 Open in New Window Polymer component 2 2
4AC 8cg8 Open in New Window Polymer component 2 2
4AC 8cgn Open in New Window Polymer component 2 2
4AC 8civ Open in New Window Polymer component 1 1
4AC 8cku Open in New Window Polymer component 2 2
4AC 8cmj Open in New Window Polymer component 2 2
4AC 8eub Open in New Window Polymer component 2 2
4AC 8evp Open in New Window Polymer component 2 2
4AC 8evq Open in New Window Polymer component 2 2
4AC 8evr Open in New Window Polymer component 2 2
4AC 8evs Open in New Window Polymer component 2 2
4AC 8evt Open in New Window Polymer component 2 2
4AC 8ewb Open in New Window Polymer component 2 2
4AC 8ewc Open in New Window Polymer component 2 2
4AC 8g5y Open in New Window Polymer component 2 2
4AC 8g5z Open in New Window Polymer component 2 2
4AC 8g60 Open in New Window Polymer component 2 2
4AC 8g61 Open in New Window Polymer component 2 2
4AC 8g6j Open in New Window Polymer component 2 2
4AC 8glp Open in New Window Polymer component 2 2
4AC 8jdj Open in New Window Polymer component 2 2
4AC 8jdk Open in New Window Polymer component 2 2
4AC 8jdl Open in New Window Polymer component 2 2
4AC 8jdm Open in New Window Polymer component 2 2
4AC 8p2k Open in New Window Polymer component 2 2
4AC 8p7b Open in New Window Polymer component 2 2
4AC 8p7c Open in New Window Polymer component 2 1
4AC 8p7d Open in New Window Polymer component 1 1
4AC 8ppk Open in New Window Polymer component 2 2
4AC 8ppl Open in New Window Polymer component 2 2
4AC 8q7z Open in New Window Polymer component 2 2
4AC 8q87 Open in New Window Polymer component 2 2
4AC 8qoi Open in New Window Polymer component 2 2
4AC 8r57 Open in New Window Polymer component 2 2
4AC 8r6f Open in New Window Polymer component 2 2
4AC 8scb Open in New Window Polymer component 2 2
4AC 9bkd Open in New Window Polymer component 2 2
4AC 9bln Open in New Window Polymer component 2 2
4AC 9f1b Open in New Window Polymer component 2 2
4AC 9f1c Open in New Window Polymer component 2 2
4AC 9f1d Open in New Window Polymer component 2 2