Chemical Components in the PDB

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DFN : Summary

Code

DFN

One-letter code

X

Molecule name

3-[3-(2,3-DIHYDROXY-PROPYLAMINO)-PHENYL]-4-(5-FLUORO-1-METHYL-1H-INDOL-3-YL)-PYRROLE-2,5-DIONE

Systematic names

ProgramVersionName
ACDLabs 10.04 3-(3-{[(2S)-2,3-dihydroxypropyl]amino}phenyl)-4-(5-fluoro-1-methyl-1H-indol-3-yl)-1H-pyrrole-2,5-dione
OpenEye OEToolkits 1.5.0 3-[3-[[(2S)-2,3-dihydroxypropyl]amino]phenyl]-4-(5-fluoro-1-methyl-indol-3-yl)pyrrole-2,5-dione

Formula

C22 H20 F N3 O4

Formal charge

0

Molecular weight

409.41 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C4C(c1cccc(NCC(O)CO)c1)=C(c3c2cc(F)ccc2n(c3)C)C(=O)N4
SMILES CACTVS 3.341 Cn1cc(c2cc(F)ccc12)C3=C(C(=O)NC3=O)c4cccc(NC[CH](O)CO)c4
SMILES OpenEye OEToolkits 1.5.0 Cn1cc(c2c1ccc(c2)F)C3=C(C(=O)NC3=O)c4cccc(c4)NCC(CO)O
Canonical SMILES CACTVS 3.341 Cn1cc(c2cc(F)ccc12)C3=C(C(=O)NC3=O)c4cccc(NC[C@H](O)CO)c4
Canonical SMILES OpenEye OEToolkits 1.5.0 Cn1cc(c2c1ccc(c2)F)C3=C(C(=O)NC3=O)c4cccc(c4)NC[C@@H](CO)O

IUPAC InChI

InChI=1S/C22H20FN3O4/c1-26-10-17(16-8-13(23)5-6-18(16)26)20-19(21(29)25-22(20)30)12-3-2-4-14(7-12)24-9-15(28)11-27/h2-8,10,15,24,27-28H,9,11H2,1H3,(H,25,29,30)/t15-/m0/s1

IUPAC InChI key

RPGZQOOZHIEPJW-HNNXBMFYSA-N
DFN

wwPDB Information

Atom count

50 (30 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2003-09-21

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



DFN : Atoms of Molecule

Total Number of Atoms: 50
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C28 C C28 N N N 0 -2.208 3.093 -2.675
2 N22 N N22 N Y N 0 -2.437 1.947 -1.792
3 C48 C C48 N Y N 0 -1.757 0.775 -1.852
4 C21 C C21 N Y N 0 -3.372 1.911 -0.776
5 C24 C C24 N Y N 0 -4.306 2.833 -0.315
6 C31 C C31 N Y N 0 -5.133 2.507 0.739
7 C29 C C29 N Y N 0 -5.047 1.261 1.347
8 F39 F F39 N N N 0 -5.864 0.958 2.379
9 C20 C C20 N Y N 0 -3.29 0.65 -0.165
10 C23 C C23 N Y N 0 -4.13 0.332 0.9
11 C19 C C19 N Y N 0 -2.225 -0.079 -0.879
12 C01 C C01 N N N 0 -1.758 -1.445 -0.607
13 C02 C C02 N N N 0 -0.577 -1.814 0.023
14 C03 C C03 N N N 0 -0.571 -3.288 0.054
15 O06 O O06 N N N 0 0.306 -3.981 0.53
16 N04 N N04 N N N 0 -1.694 -3.738 -0.529
17 C05 C C05 N N N 0 -2.456 -2.71 -0.942
18 O07 O O07 N N N 0 -3.529 -2.803 -1.503
19 C08 C C08 N Y N 0 0.465 -0.911 0.553
20 C09 C C09 N Y N 0 1.743 -0.911 -0.008
21 C10 C C10 N Y N 0 2.714 -0.057 0.492
22 C11 C C11 N Y N 0 2.417 0.787 1.556
23 C12 C C12 N Y N 0 1.152 0.782 2.116
24 C13 C C13 N Y N 0 0.177 -0.059 1.623
25 N15 N N15 N N N 0 3.993 -0.049 -0.07
26 C26 C C26 N N N 0 5.021 0.849 0.463
27 C34 C C34 S N N 0 6.32 0.661 -0.324
28 O41 O O41 N N N 0 6.76 -0.693 -0.201
29 C40 C C40 N N N 0 7.393 1.599 0.232
30 O45 O O45 N N N 0 8.569 1.509 -0.576
31 H281 H 1H28 N N N 0 -2.847 3.008 -3.554
32 H282 H 2H28 N N N 0 -2.443 4.015 -2.144
33 H283 H 3H28 N N N 0 -1.163 3.109 -2.986
34 H48 H H48 N N N 0 -0.969 0.547 -2.556
35 H24 H H24 N N N 0 -4.382 3.804 -0.78
36 H31 H H31 N N N 0 -5.854 3.228 1.096
37 H23 H H23 N N N 0 -4.064 -0.637 1.373
38 H04 H H04 N N N 0 -1.926 -4.674 -0.633
39 H09 H H09 N N N 0 1.972 -1.567 -0.835
40 H11 H H11 N N N 0 3.176 1.448 1.947
41 H12 H H12 N N N 0 0.927 1.44 2.942
42 H13 H H13 N N N 0 -0.809 -0.059 2.062
43 H15 H H15 N N N 0 4.201 -0.637 -0.812
44 H261 H 1H26 N N N 0 4.685 1.882 0.369
45 H262 H 2H26 N N N 0 5.196 0.618 1.513
46 H34 H H34 N N N 0 6.144 0.892 -1.375
47 H41 H H41 N N N 0 6.903 -0.855 0.741
48 H401 H 1H40 N N N 0 7.022 2.624 0.22
49 H402 H 2H40 N N N 0 7.632 1.311 1.255
50 H45 H H45 N N N 0 9.218 2.114 -0.192



DFN : Chemical Bonds

Total Number of Bonds: 53
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C28 N22 C N sing 1.46 N N
2 C28 H281 C H sing 1.09 N N
3 C28 H282 C H sing 1.09 N N
4 C28 H283 C H sing 1.09 N N
5 N22 C48 N C sing 1.36 N Y
6 N22 C21 N C sing 1.38 N Y
7 C48 C19 C C doub 1.38 N Y
8 C48 H48 C H sing 1.08 N N
9 C21 C24 C C doub 1.39 N Y
10 C21 C20 C C sing 1.4 N Y
11 C24 C31 C C sing 1.38 N Y
12 C24 H24 C H sing 1.08 N N
13 C31 C29 C C doub 1.39 N Y
14 C31 H31 C H sing 1.08 N N
15 C29 F39 C F sing 1.35 N N
16 C29 C23 C C sing 1.38 N Y
17 C20 C23 C C doub 1.39 N Y
18 C20 C19 C C sing 1.47 N Y
19 C23 H23 C H sing 1.08 N N
20 C19 C01 C C sing 1.47 N N
21 C01 C02 C C doub 1.39 N N
22 C01 C05 C C sing 1.48 N N
23 C02 C03 C C sing 1.47 N N
24 C02 C08 C C sing 1.48 N N
25 C03 O06 C O doub 1.21 N N
26 C03 N04 C N sing 1.34 N N
27 N04 C05 N C sing 1.34 N N
28 N04 H04 N H sing 0.97 N N
29 C05 O07 C O doub 1.21 N N
30 C08 C09 C C doub 1.4 N Y
31 C08 C13 C C sing 1.4 N Y
32 C09 C10 C C sing 1.39 N Y
33 C09 H09 C H sing 1.08 N N
34 C10 C11 C C doub 1.39 N Y
35 C10 N15 C N sing 1.4 N N
36 C11 C12 C C sing 1.38 N Y
37 C11 H11 C H sing 1.08 N N
38 C12 C13 C C doub 1.38 N Y
39 C12 H12 C H sing 1.08 N N
40 C13 H13 C H sing 1.08 N N
41 N15 C26 N C sing 1.47 N N
42 N15 H15 N H sing 0.97 N N
43 C26 C34 C C sing 1.53 N N
44 C26 H261 C H sing 1.09 N N
45 C26 H262 C H sing 1.09 N N
46 C34 O41 C O sing 1.43 N N
47 C34 C40 C C sing 1.53 N N
48 C34 H34 C H sing 1.09 N N
49 O41 H41 O H sing 0.97 N N
50 C40 O45 C O sing 1.43 N N
51 C40 H401 C H sing 1.09 N N
52 C40 H402 C H sing 1.09 N N
53 O45 H45 O H sing 0.97 N N



DFN : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
DFN 1r0e Open in New Window Bound ligand 2 1