Chemical Components in the PDB

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DCZ : Summary

Code

DCZ

One-letter code

X

Molecule name

2'-DEOXYCYTIDINE

Systematic names

ProgramVersionName
ACDLabs 10.04 2'-deoxycytidine
OpenEye OEToolkits 1.5.0 4-amino-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one

Formula

C9 H13 N3 O4

Formal charge

0

Molecular weight

227.217 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C1N=C(N)C=CN1C2OC(C(O)C2)CO
SMILES CACTVS 3.341 NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO)O2
SMILES OpenEye OEToolkits 1.5.0 C1C(C(OC1N2C=CC(=NC2=O)N)CO)O
Canonical SMILES CACTVS 3.341 NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO)O2
Canonical SMILES OpenEye OEToolkits 1.5.0 C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)CO)O

IUPAC InChI

InChI=1S/C9H13N3O4/c10-7-1-2-12(9(15)11-7)8-3-5(14)6(4-13)16-8/h1-2,5-6,8,13-14H,3-4H2,(H2,10,11,15)/t5-,6+,8+/m0/s1

IUPAC InChI key

CKTSBUTUHBMZGZ-SHYZEUOFSA-N
DCZ

wwPDB Information

Atom count

29 (16 without Hydrogen)

Polymer type

Deoxy ribonucleotide

Type description

DNA OH 5 prime terminus

Type code

ATOMN

Is modified

No

Standard parent

Not Assigned

Defined at

2001-05-30

Last modified at

2017-07-13

Status

Released

Obsoleted

Not Assigned



DCZ : Atoms of Molecule

Total Number of Atoms: 29
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 -0.234 -0.603 1.003
2 C2 C C2 N N N 0 0.076 0.676 1.279
3 N3 N N3 N N N 0 0.313 1.072 2.528
4 C4 C C4 N N N 0 0.248 0.212 3.535
5 C5 C C5 N N N 0 -0.068 -1.137 3.279
6 C6 C C6 N N N 0 -0.312 -1.523 2.005
7 O2 O O2 N N N 0 0.142 1.487 0.37
8 N4 N N4 N N N 0 0.495 0.632 4.822
9 C1' C C1* R N N 0 -0.489 -1.009 -0.381
10 C2' C C2* N N N 0 -1.673 -0.205 -0.952
11 C3' C C3* S N N 0 -1.082 0.514 -2.188
12 C4' C C4* R N N 0 0.165 -0.35 -2.502
13 O4' O O4* N N N 0 0.659 -0.72 -1.195
14 O3' O O3* N N N 0 -2.004 0.494 -3.28
15 C5' C C5* N N N 0 1.209 0.466 -3.266
16 O5' O O5* N N N 0 2.346 -0.352 -3.542
17 H5 H H5 N N N 0 -0.125 -1.85 4.089
18 H6 H H6 N N N 0 -0.562 -2.551 1.784
19 HN41 H 1HN4 N N N 0 0.718 1.56 4.994
20 HN42 H 2HN4 N N N 0 0.444 0.001 5.556
21 H1' H H1* N N N 0 -0.712 -2.075 -0.419
22 H2'1 H 1H2* N N N 0 -2.48 -0.875 -1.25
23 H2'2 H 2H2* N N N 0 -2.03 0.52 -0.222
24 H3' H H3* N N N 0 -0.795 1.536 -1.943
25 H4' H H4* N N N 0 -0.115 -1.238 -3.069
26 HO3' H *HO3 N N N 0 -2.793 0.97 -2.987
27 H5'1 H 1H5* N N N 0 0.779 0.819 -4.203
28 H5'2 H 2H5* N N N 0 1.514 1.321 -2.662
29 HO51 H 1HO5 N N N 0 2.978 0.199 -4.022



DCZ : Chemical Bonds

Total Number of Bonds: 30
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N1 C2 N C sing 1.34 N N
2 N1 C6 N C sing 1.36 N N
3 N1 C1' N C sing 1.46 N N
4 C2 N3 C N sing 1.33 N N
5 C2 O2 C O doub 1.22 N N
6 N3 C4 N C doub 1.33 N N
7 C4 C5 C C sing 1.41 N N
8 C4 N4 C N sing 1.38 N N
9 C5 C6 C C doub 1.35 N N
10 C5 H5 C H sing 1.08 N N
11 C6 H6 C H sing 1.08 N N
12 N4 HN41 N H sing 0.97 N N
13 N4 HN42 N H sing 0.97 N N
14 C1' C2' C C sing 1.54 N N
15 C1' O4' C O sing 1.44 N N
16 C1' H1' C H sing 1.09 N N
17 C2' C3' C C sing 1.55 N N
18 C2' H2'1 C H sing 1.09 N N
19 C2' H2'2 C H sing 1.09 N N
20 C3' C4' C C sing 1.55 N N
21 C3' O3' C O sing 1.43 N N
22 C3' H3' C H sing 1.09 N N
23 C4' O4' C O sing 1.45 N N
24 C4' C5' C C sing 1.53 N N
25 C4' H4' C H sing 1.09 N N
26 O3' HO3' O H sing 0.97 N N
27 C5' O5' C O sing 1.43 N N
28 C5' H5'1 C H sing 1.09 N N
29 C5' H5'2 C H sing 1.09 N N
30 O5' HO51 O H sing 0.97 N N



DCZ : Used in PDB Entries

Total Number of PDB Entries: 29
Ligand Code PDB Entry ID Type Total Distinct
DCZ 1j90 Open in New Window Bound ligand 2 1
DCZ 1p60 Open in New Window Bound ligand 2 1
DCZ 1p61 Open in New Window Bound ligand 1 1
DCZ 1rmy Open in New Window Bound ligand 2 1
DCZ 1vq5 Open in New Window Polymer component 1 1
DCZ 1vqp Open in New Window Polymer component 1 1
DCZ 2a2z Open in New Window Bound ligand 4 1
DCZ 2a30 Open in New Window Bound ligand 4 1
DCZ 2no1 Open in New Window Bound ligand 2 1
DCZ 2vp5 Open in New Window Bound ligand 2 1
DCZ 2z6q Open in New Window Bound ligand 1 1
DCZ 3qba Open in New Window Polymer component 2 1
DCZ 3ugw Open in New Window Bound ligand 1 1
DCZ 5fbd Open in New Window Bound ligand 1 1
DCZ 5fbg Open in New Window Bound ligand 2 1
DCZ 5ocz Open in New Window Polymer component 2 1
DCZ 5odf Open in New Window Polymer component 2 1
DCZ 5odm Open in New Window Polymer component 2 1
DCZ 5oe1 Open in New Window Polymer component 2 1
DCZ 6als Open in New Window Polymer component 2 1
DCZ 6alt Open in New Window Polymer component 2 1
DCZ 6alu Open in New Window Polymer component 2 1
DCZ 6nka Open in New Window Bound ligand 4 1
DCZ 6rio Open in New Window Polymer component 2 1
DCZ 7d0y Open in New Window Polymer component 1 1
DCZ 7d0z Open in New Window Polymer component 1 1
DCZ 7kwl Open in New Window Polymer component 2 1
DCZ 7kwr Open in New Window Polymer component 2 1
DCZ 8qxl Open in New Window Bound ligand 2 1