Chemical Components in the PDB

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DCF : Summary

Code

DCF

One-letter code

X

Molecule name

2'-DEOXYCOFORMYCIN

Systematic names

ProgramVersionName
ACDLabs 10.04 (8R)-3-(2-deoxy-beta-D-erythro-pentofuranosyl)-3,6,7,8-tetrahydroimidazo[4,5-d][1,3]diazepin-8-ol
OpenEye OEToolkits 1.5.0 (8R)-3-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-7,8-dihydro-6H-imidazo[4,5-f][1,3]diazepin-8-ol

Formula

C11 H16 N4 O4

Formal charge

0

Molecular weight

268.269 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 n2c1c(N=CNCC1O)n(c2)C3OC(C(O)C3)CO
SMILES CACTVS 3.341 OC[CH]1O[CH](C[CH]1O)n2cnc3[CH](O)CNC=Nc23
SMILES OpenEye OEToolkits 1.5.0 c1nc2c(n1C3CC(C(O3)CO)O)N=CNCC2O
Canonical SMILES CACTVS 3.341 OC[C@H]1O[C@H](C[C@@H]1O)n2cnc3[C@H](O)CNC=Nc23
Canonical SMILES OpenEye OEToolkits 1.5.0 c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)CO)O)N=CNC[C@H]2O

IUPAC InChI

InChI=1S/C11H16N4O4/c16-3-8-6(17)1-9(19-8)15-5-14-10-7(18)2-12-4-13-11(10)15/h4-9,16-18H,1-3H2,(H,12,13)/t6-,7+,8+,9+/m0/s1

IUPAC InChI key

FPVKHBSQESCIEP-JQCXWYLXSA-N
DCF

wwPDB Information

Atom count

35 (19 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

1999-07-08

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



DCF : Atoms of Molecule

Total Number of Atoms: 35
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C10 C C10 N Y N 0 -0.284 0.108 -1.387
2 C1S C C1S R N N 0 -0.494 0.404 1.131
3 C2 C C2 N Y N 0 1.419 -0.589 -0.17
4 C2S C C2S N N N 0 -1.341 -0.759 1.68
5 C3S C C3S S N N 0 -0.791 -0.989 3.111
6 C4S C C4S R N N 0 -0.1 0.364 3.413
7 C5 C C5 N N N 0 -2.026 0.868 -2.814
8 C5S C C5S N N N 0 0.997 0.186 4.463
9 C7 C C7 N N N 0 -0.108 0.584 -4.353
10 C8 C C8 R N N 0 0.658 -0.544 -3.692
11 C9 C C9 N Y N 0 0.67 -0.409 -2.195
12 H1S H H1S N N N 0 -1.133 1.262 0.923
13 H2 H H2 N N N 0 2.061 -0.818 0.667
14 H2S1 H 1H2S N N N 0 -2.393 -0.48 1.719
15 H2S2 H 2H2S N N N 0 -1.204 -1.651 1.069
16 H3S H H3S N N N 0 -0.066 -1.804 3.123
17 H4S H H4S N N N 0 -0.83 1.102 3.744
18 H5 H H5 N N N 0 -2.988 1.359 -2.812
19 H5S1 H 1H5S N N N 0 1.724 -0.544 4.109
20 H5S2 H 2H5S N N N 0 0.555 -0.162 5.396
21 H71 H 1H7 N N N 0 0.302 1.537 -4.019
22 H72 H 2H7 N N N 0 0.0040 0.507 -5.434
23 H8 H H8 N N N 0 0.193 -1.493 -3.959
24 HN6 H HN6 N N N 0 -2.135 0.237 -4.704
25 HO3 H HO3 N N N 0 -2.297 -2.048 3.732
26 HO5 H HO5 N N N 0 2.334 1.282 5.352
27 HO8 H HO8 N N N 0 1.959 -0.622 -5.134
28 N1 N N1 N Y N 0 1.693 -0.821 -1.421
29 N3 N N3 N Y N 0 0.195 -0.01 -0.092
30 N4 N N4 N N N 0 -1.483 0.664 -1.679
31 N6 N N6 N N N 0 -1.517 0.532 -4.017
32 O3S O O3S N N N 0 -1.854 -1.242 4.031
33 O4S O O4S N N N 0 0.468 0.747 2.142
34 O5S O O5S N N N 0 1.651 1.438 4.685
35 O8 O O8 N N N 0 2.004 -0.534 -4.172



DCF : Chemical Bonds

Total Number of Bonds: 37
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N1 C2 N C doub 1.3 N Y
2 N1 C9 N C sing 1.35 N Y
3 C2 N3 C N sing 1.36 N Y
4 C2 H2 C H sing 1.08 N N
5 N3 C10 N C sing 1.39 N Y
6 N3 C1S N C sing 1.46 N N
7 C9 C10 C C doub 1.35 N Y
8 C9 C8 C C sing 1.5 N N
9 C10 N4 C N sing 1.35 N N
10 N4 C5 N C doub 1.27 N N
11 C5 N6 C N sing 1.35 N N
12 C5 H5 C H sing 1.08 N N
13 N6 C7 N C sing 1.45 N N
14 N6 HN6 N H sing 0.97 N N
15 C7 C8 C C sing 1.52 N N
16 C7 H71 C H sing 1.09 N N
17 C7 H72 C H sing 1.09 N N
18 C8 O8 C O sing 1.43 N N
19 C8 H8 C H sing 1.09 N N
20 O8 HO8 O H sing 0.97 N N
21 C2S C3S C C sing 1.55 N N
22 C2S C1S C C sing 1.54 N N
23 C2S H2S1 C H sing 1.09 N N
24 C2S H2S2 C H sing 1.09 N N
25 C3S O3S C O sing 1.43 N N
26 C3S C4S C C sing 1.55 N N
27 C3S H3S C H sing 1.09 N N
28 O3S HO3 O H sing 0.97 N N
29 O5S C5S O C sing 1.43 N N
30 O5S HO5 O H sing 0.97 N N
31 C5S C4S C C sing 1.53 N N
32 C5S H5S1 C H sing 1.09 N N
33 C5S H5S2 C H sing 1.09 N N
34 C4S O4S C O sing 1.44 N N
35 C4S H4S C H sing 1.09 N N
36 O4S C1S O C sing 1.44 N N
37 C1S H1S C H sing 1.09 N N



DCF : Used in PDB Entries

Total Number of PDB Entries: 4
Ligand Code PDB Entry ID Type Total Distinct
DCF 1a4l Open in New Window Bound ligand 4 1
DCF 2pgr Open in New Window Bound ligand 1 1
DCF 6n91 Open in New Window Bound ligand 2 1
DCF 6n9m Open in New Window Bound ligand 1 1