Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

CDY : Summary

Code

CDY

One-letter code

X

Molecule name

2-CHLORODIDEOXYADENOSINE

Systematic names

ProgramVersionName
ACDLabs 10.04 [(2S,5R)-5-(6-amino-2-chloro-9H-purin-9-yl)tetrahydrofuran-2-yl]methanol
OpenEye OEToolkits 1.5.0 [(2S,5R)-5-(6-amino-2-chloro-purin-9-yl)oxolan-2-yl]methanol

Formula

C10 H12 Cl N5 O2

Formal charge

0

Molecular weight

269.688 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 Clc1nc(c2ncn(c2n1)C3OC(CC3)CO)N
SMILES CACTVS 3.341 Nc1nc(Cl)nc2n(cnc12)[CH]3CC[CH](CO)O3
SMILES OpenEye OEToolkits 1.5.0 c1nc2c(nc(nc2n1C3CCC(O3)CO)Cl)N
Canonical SMILES CACTVS 3.341 Nc1nc(Cl)nc2n(cnc12)[C@H]3CC[C@@H](CO)O3
Canonical SMILES OpenEye OEToolkits 1.5.0 c1nc2c(nc(nc2n1[C@H]3CC[C@H](O3)CO)Cl)N

IUPAC InChI

InChI=1S/C10H12ClN5O2/c11-10-14-8(12)7-9(15-10)16(4-13-7)6-2-1-5(3-17)18-6/h4-6,17H,1-3H2,(H2,12,14,15)/t5-,6+/m0/s1

IUPAC InChI key

FNLILOONPKMGST-NTSWFWBYSA-N
CDY

wwPDB Information

Atom count

30 (18 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2003-09-11

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



CDY : Atoms of Molecule

Total Number of Atoms: 30
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O5' O O5* N N N 0 0.155 -1.423 -5.521
2 C5' C C5* N N N 0 0.072 -0.054 -5.118
3 C4' C C4* S N N 0 -0.773 0.052 -3.848
4 O4' O O4* N N N 0 -0.114 -0.599 -2.741
5 C3' C C3* N N N 0 -0.879 1.528 -3.387
6 C2' C C2* N N N 0 -1.164 1.375 -1.873
7 C1' C C1* R N N 0 -0.668 -0.043 -1.536
8 N9 N N9 N Y N 0 0.363 0.022 -0.498
9 C8 C C8 N Y N 0 1.705 0.146 -0.701
10 N7 N N7 N Y N 0 2.327 0.173 0.441
11 C5 C C5 N Y N 0 1.425 0.075 1.447
12 C4 C C4 N Y N 0 0.155 -0.029 0.856
13 N1 N N1 N Y N 0 0.386 -0.073 3.55
14 N3 N N3 N Y N 0 -0.914 -0.142 1.638
15 C2 C C2 N Y N 0 -0.787 -0.163 2.949
16 CL CL CL N N N 0 -2.216 -0.313 3.924
17 C6 C C6 N Y N 0 1.509 0.043 2.85
18 N6 N N6 N N N 0 2.734 0.136 3.487
19 HO5 H HO5 N N N 0 0.695 -1.446 -6.323
20 HC51 H 1HC5 N N N 0 -0.388 0.53 -5.913
21 HC52 H 2HC5 N N N 0 1.074 0.326 -4.921
22 H4' H H4* N N N 0 -1.764 -0.37 -4.011
23 HC31 H 1HC3 N N N 0 -1.704 2.034 -3.889
24 HC32 H 2HC3 N N N 0 0.058 2.057 -3.554
25 HC21 H 1HC2 N N N 0 -2.233 1.462 -1.675
26 HC22 H 2HC2 N N N 0 -0.608 2.119 -1.303
27 H1' H H1* N N N 0 -1.501 -0.656 -1.192
28 HC8 H HC8 N N N 0 2.182 0.211 -1.668
29 HN61 H 1HN6 N N N 0 2.779 0.117 4.456
30 HN62 H 2HN6 N N N 0 3.548 0.217 2.965



CDY : Chemical Bonds

Total Number of Bonds: 32
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O5' C5' O C sing 1.43 N N
2 O5' HO5 O H sing 0.97 N N
3 C5' C4' C C sing 1.53 N N
4 C5' HC51 C H sing 1.09 N N
5 C5' HC52 C H sing 1.09 N N
6 C4' O4' C O sing 1.44 N N
7 C4' C3' C C sing 1.55 N N
8 C4' H4' C H sing 1.09 N N
9 O4' C1' O C sing 1.44 N N
10 C3' C2' C C sing 1.55 N N
11 C3' HC31 C H sing 1.09 N N
12 C3' HC32 C H sing 1.09 N N
13 C2' C1' C C sing 1.54 N N
14 C2' HC21 C H sing 1.09 N N
15 C2' HC22 C H sing 1.09 N N
16 C1' N9 C N sing 1.46 N N
17 C1' H1' C H sing 1.09 N N
18 N9 C8 N C sing 1.36 N Y
19 N9 C4 N C sing 1.37 N Y
20 C8 N7 C N doub 1.3 N Y
21 C8 HC8 C H sing 1.08 N N
22 N7 C5 N C sing 1.35 N Y
23 C5 C4 C C doub 1.4 N Y
24 C5 C6 C C sing 1.41 N Y
25 C4 N3 C N sing 1.33 N Y
26 N3 C2 N C doub 1.32 N Y
27 C2 CL C CL sing 1.74 N N
28 C2 N1 C N sing 1.32 N Y
29 N1 C6 N C doub 1.33 N Y
30 C6 N6 C N sing 1.38 N N
31 N6 HN61 N H sing 0.97 N N
32 N6 HN62 N H sing 0.97 N N



CDY : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
CDY 1qye Open in New Window Bound ligand 1 1