Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

NEI : Summary

Code

NEI

One-letter code

X

Molecule name

(2S,3S,4R,5R)-5-(6-AMINO-2-IODO-9H-PURIN-9-YL)-N-ETHYL-3,4-DIHYDROXYTETRAHYDROFURAN-2-CARBOXAMIDE

Systematic names

ProgramVersionName
ACDLabs 10.04 (2S,3S,4R,5R)-5-(6-amino-2-iodo-9H-purin-9-yl)-N-ethyl-3,4-dihydroxytetrahydrofuran-2-carboxamide (non-preferred name)
OpenEye OEToolkits 1.5.0 (2S,3S,4R,5R)-5-(6-amino-2-iodo-purin-9-yl)-N-ethyl-3,4-dihydroxy-oxolane-2-carboxamide

Formula

C12 H15 I N6 O4

Formal charge

0

Molecular weight

434.19 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 Ic1nc(c2ncn(c2n1)C3OC(C(=O)NCC)C(O)C3O)N
SMILES CACTVS 3.341 CCNC(=O)[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)nc(I)nc23
SMILES OpenEye OEToolkits 1.5.0 CCNC(=O)C1C(C(C(O1)n2cnc3c2nc(nc3N)I)O)O
Canonical SMILES CACTVS 3.341 CCNC(=O)[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)nc(I)nc23
Canonical SMILES OpenEye OEToolkits 1.5.0 CCNC(=O)[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2nc(nc3N)I)O)O

IUPAC InChI

InChI=1S/C12H15IN6O4/c1-2-15-10(22)7-5(20)6(21)11(23-7)19-3-16-4-8(14)17-12(13)18-9(4)19/h3,5-7,11,20-21H,2H2,1H3,(H,15,22)(H2,14,17,18)/t5-,6+,7-,11+/m0/s1

IUPAC InChI key

YEBHQRSEUJCFMN-QMWPFBOUSA-N
NEI

wwPDB Information

Atom count

38 (23 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2006-06-16

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



NEI : 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 C52 C C52 N N N 0 8.6 0.895 0.136
2 C51 C C51 N N N 0 7.523 -0.093 -0.317
3 N5' N N5* N N N 0 6.21 0.553 -0.251
4 C5' C C5* N N N 0 5.104 -0.132 -0.606
5 O5' O O5* N N N 0 5.197 -1.282 -0.98
6 C4' C C4* S N N 0 3.753 0.532 -0.539
7 O4' O O4* N N N 0 2.72 -0.369 -0.993
8 C3' C C3* S N N 0 3.361 0.824 0.932
9 O3' O O3* N N N 0 3.887 2.08 1.367
10 C2' C C2* R N N 0 1.814 0.87 0.851
11 O2' O O2* N N N 0 1.359 2.222 0.764
12 C1' C C1* R N N 0 1.479 0.103 -0.443
13 N9 N N9 N Y N 0 0.604 -1.032 -0.14
14 C8 C C8 N Y N 0 1.001 -2.315 0.096
15 N7 N N7 N Y N 0 -0.037 -3.065 0.331
16 C5 C C5 N Y N 0 -1.162 -2.313 0.261
17 C4 C C4 N Y N 0 -0.763 -0.999 -0.036
18 N3 N N3 N Y N 0 -1.691 -0.056 -0.167
19 C2 C C2 N Y N 0 -2.967 -0.344 -0.009
20 I2 I I2 N N N 0 -4.379 1.189 -0.219
21 N1 N N1 N Y N 0 -3.388 -1.563 0.276
22 C6 C C6 N Y N 0 -2.534 -2.571 0.419
23 N6 N N6 N N N 0 -2.985 -3.844 0.719
24 H521 H 1H52 N N N 0 8.399 1.207 1.161
25 H522 H 2H52 N N N 0 9.577 0.415 0.087
26 H523 H 3H52 N N N 0 8.591 1.768 -0.517
27 H511 H 1H51 N N N 0 7.724 -0.404 -1.342
28 H512 H 2H51 N N N 0 7.532 -0.965 0.336
29 HN5' H HN5* N N N 0 6.136 1.472 0.048
30 H4' H H4* N N N 0 3.747 1.45 -1.127
31 H3' H H3* N N N 0 3.693 0.019 1.588
32 HO3' H HO3* N N N 0 4.849 1.986 1.396
33 H2' H H2* N N N 0 1.371 0.374 1.715
34 HO2' H HO2* N N N 0 1.595 2.651 1.598
35 H1' H H1* N N N 0 0.989 0.77 -1.152
36 H8 H H8 N N N 0 2.025 -2.659 0.089
37 HN61 H 1HN6 N N N 0 -2.351 -4.572 0.821
38 HN62 H 2HN6 N N N 0 -3.935 -4.01 0.826



NEI : Chemical Bonds

Total Number of Bonds: 40
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C52 C51 C C sing 1.53 N N
2 C52 H521 C H sing 1.09 N N
3 C52 H522 C H sing 1.09 N N
4 C52 H523 C H sing 1.09 N N
5 C51 N5' C N sing 1.46 N N
6 C51 H511 C H sing 1.09 N N
7 C51 H512 C H sing 1.09 N N
8 N5' C5' N C sing 1.35 N N
9 N5' HN5' N H sing 0.97 N N
10 C5' O5' C O doub 1.21 N N
11 C5' C4' C C sing 1.51 N N
12 C4' O4' C O sing 1.44 N N
13 C4' C3' C C sing 1.55 N N
14 C4' H4' C H sing 1.09 N N
15 O4' C1' O C sing 1.44 N N
16 C3' O3' C O sing 1.43 N N
17 C3' C2' C C sing 1.55 N N
18 C3' H3' C H sing 1.09 N N
19 O3' HO3' O H sing 0.97 N N
20 C2' O2' C O sing 1.43 N N
21 C2' C1' C C sing 1.54 N N
22 C2' H2' C H sing 1.09 N N
23 O2' HO2' O H sing 0.97 N N
24 C1' N9 C N sing 1.46 N N
25 C1' H1' C H sing 1.09 N N
26 N9 C8 N C sing 1.36 N Y
27 N9 C4 N C sing 1.37 N Y
28 C8 N7 C N doub 1.3 N Y
29 C8 H8 C H sing 1.08 N N
30 N7 C5 N C sing 1.36 N Y
31 C5 C4 C C sing 1.4 N Y
32 C5 C6 C C doub 1.4 N Y
33 C4 N3 C N doub 1.33 N Y
34 N3 C2 N C sing 1.32 N Y
35 C2 I2 C I sing 2.09 N N
36 C2 N1 C N doub 1.32 N Y
37 N1 C6 N C sing 1.33 N Y
38 C6 N6 C N sing 1.38 N N
39 N6 HN61 N H sing 0.97 N N
40 N6 HN62 N H sing 0.97 N N



NEI : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
NEI 2h8m Open in New Window Bound ligand 2 1