Chemical Components in the PDB

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1CC : Summary

Code

1CC

One-letter code

C

Molecule name

5-carboxy-2'-deoxycytidine monophosphate

Systematic names

ProgramVersionName
ACDLabs 12.01 5-carboxy-2'-deoxycytidine 5'-(dihydrogen phosphate)
OpenEye OEToolkits 1.7.6 4-azanyl-2-oxidanylidene-1-[(2R,4S,5R)-4-oxidanyl-5-(phosphonooxymethyl)oxolan-2-yl]pyrimidine-5-carboxylic acid

Formula

C10 H14 N3 O9 P

Formal charge

0

Molecular weight

351.207 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(O)C=1C(=NC(=O)N(C=1)C2OC(C(O)C2)COP(=O)(O)O)N
SMILES CACTVS 3.370 NC1=NC(=O)N(C=C1C(O)=O)[CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2
SMILES OpenEye OEToolkits 1.7.6 C1C(C(OC1N2C=C(C(=NC2=O)N)C(=O)O)COP(=O)(O)O)O
Canonical SMILES CACTVS 3.370 NC1=NC(=O)N(C=C1C(O)=O)[C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2
Canonical SMILES OpenEye OEToolkits 1.7.6 C1[C@@H]([C@H](O[C@H]1N2C=C(C(=NC2=O)N)C(=O)O)COP(=O)(O)O)O

IUPAC InChI

InChI=1S/C10H14N3O9P/c11-8-4(9(15)16)2-13(10(17)12-8)7-1-5(14)6(22-7)3-21-23(18,19)20/h2,5-7,14H,1,3H2,(H,15,16)(H2,11,12,17)(H2,18,19,20)/t5-,6+,7+/m0/s1

IUPAC InChI key

WEUNVGZSKGOUOC-RRKCRQDMSA-N
1CC

wwPDB Information

Atom count

37 (23 without Hydrogen)

Polymer type

Deoxy ribonucleotide

Type description

DNA LINKING

Type code

ATOMN

Is modified

Yes

Standard parent

DC

Defined at

2011-11-17

Last modified at

2012-02-10

Status

Released

Obsoleted

Not Assigned



1CC : Atoms of Molecule

Total Number of Atoms: 37
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 P P P N N N 0 4.735 1.13 0.305
2 OP1 O OP1 N N N 0 5.879 0.231 0.03
3 OP2 O OP2 N N N 0 4.466 2.064 -0.978
4 O5' O O5' N N N 0 3.423 0.249 0.612
5 C5' C C5' N N N 0 2.928 -0.748 -0.284
6 C4' C C4' R N N 0 1.673 -1.391 0.312
7 C3' C C3' S N N 0 1.169 -2.532 -0.6
8 C2' C C2' N N N 0 -0.37 -2.427 -0.517
9 C1' C C1' R N N 0 -0.614 -1.235 0.435
10 O4' O O4' N N N 0 0.589 -0.438 0.348
11 N1 N N1 N N N 0 -1.774 -0.459 -0.0070
12 C6 C C6 N N N 0 -2.872 -0.406 0.775
13 C5 C C5 N N N 0 -3.964 0.33 0.349
14 C4 C C4 N N N 0 -3.867 1.02 -0.942
15 N4 N N4 N N N 0 -4.916 1.766 -1.418
16 N3 N N3 N N N 0 -2.746 0.909 -1.641
17 C2 C C2 N N N 0 -1.723 0.192 -1.18
18 O2 O O2 N N N 0 -0.709 0.114 -1.852
19 C21 C C21 N N N 0 -5.184 0.418 1.166
20 O22 O O22 N N N 0 -5.285 -0.242 2.181
21 O23 O O23 N N N 0 -6.191 1.232 0.789
22 O3' O O3' N N N 0 1.612 -3.799 -0.108
23 HOP2 H HOP2 N N N 0 3.729 2.68 -0.869
24 H5'' H H5'' N N N 0 2.68 -0.287 -1.24
25 H5' H H5' N N N 0 3.69 -1.512 -0.436
26 H4' H H4' N N N 0 1.881 -1.769 1.313
27 H3' H H3' N N N 0 1.51 -2.381 -1.625
28 H2'' H H2'' N N N 0 -0.791 -2.222 -1.501
29 H2' H H2' N N N 0 -0.794 -3.341 -0.101
30 H1' H H1' N N N 0 -0.759 -1.589 1.456
31 H6 H H6 N N N 0 -2.899 -0.93 1.719
32 H42 H H42 N N N 0 -5.701 1.905 -0.866
33 H41 H H41 N N N 0 -4.873 2.154 -2.306
34 H5 H H5 N N N 0 -6.973 1.256 1.357
35 HO3' H HO3' N N N 0 1.324 -4.551 -0.643
36 OP3 O OP3 N N Y 0 5.072 2.053 1.58
37 HOP3 H HOP3 N N N 0 5.853 2.612 1.465



1CC : Chemical Bonds

Total Number of Bonds: 38
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O22 C21 O C doub 1.21 N N
2 N4 C4 N C sing 1.37 N N
3 C21 O23 C O sing 1.35 N N
4 C21 C5 C C sing 1.47 N N
5 OP1 P O P doub 1.48 N N
6 C4 C5 C C sing 1.47 N N
7 C4 N3 C N doub 1.33 N N
8 C5 C6 C C doub 1.38 N N
9 N3 C2 N C sing 1.33 N N
10 OP2 P O P sing 1.61 N N
11 C6 N1 C N sing 1.35 N N
12 P O5' P O sing 1.61 N N
13 C2 N1 C N sing 1.34 N N
14 C2 O2 C O doub 1.22 N N
15 N1 C1' N C sing 1.46 N N
16 O5' C5' O C sing 1.43 N N
17 C5' C4' C C sing 1.53 N N
18 C2' C1' C C sing 1.54 N N
19 C2' C3' C C sing 1.54 N N
20 C1' O4' C O sing 1.45 N N
21 C3' C4' C C sing 1.55 N N
22 C3' O3' C O sing 1.43 N N
23 O4' C4' O C sing 1.44 N N
24 OP2 HOP2 O H sing 0.97 N N
25 C5' H5'' C H sing 1.09 N N
26 C5' H5' C H sing 1.09 N N
27 C4' H4' C H sing 1.09 N N
28 C3' H3' C H sing 1.09 N N
29 C2' H2'' C H sing 1.09 N N
30 C2' H2' C H sing 1.09 N N
31 C1' H1' C H sing 1.09 N N
32 C6 H6 C H sing 1.08 N N
33 N4 H42 N H sing 0.97 N N
34 N4 H41 N H sing 0.97 N N
35 O23 H5 O H sing 0.97 N N
36 O3' HO3' O H sing 0.97 N N
37 P OP3 P O sing 1.61 N N
38 OP3 HOP3 O H sing 0.97 N N



1CC : Used in PDB Entries

Total Number of PDB Entries: 15
Ligand Code PDB Entry ID Type Total Distinct
1CC 3uo7 Open in New Window Polymer component 1 1
1CC 4m9v Open in New Window Polymer component 2 1
1CC 4pwm Open in New Window Polymer component 2 1
1CC 4r2r Open in New Window Polymer component 1 1
1CC 4y52 Open in New Window Polymer component 1 1
1CC 4y7n Open in New Window Polymer component 1 1
1CC 5exh Open in New Window Polymer component 2 1
1CC 5eyo Open in New Window Polymer component 2 1
1CC 5kl5 Open in New Window Polymer component 1 1
1CC 5kl7 Open in New Window Polymer component 1 1
1CC 5zat Open in New Window Polymer component 2 1
1CC 6n2r Open in New Window Polymer component 1 1
1CC 6n2s Open in New Window Polymer component 1 1
1CC 6od5 Open in New Window Polymer component 8 2
1CC 6u16 Open in New Window Polymer component 1 1