Chemical Components in the PDB

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DJ3 : Summary

Code

DJ3

One-letter code

X

Molecule name

5S-5,6-oxido-7,9-trans-11,14-cis-eicosatetraenoic acid

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.6 4-[(2~{S},3~{S})-3-[(1~{E},3~{E},5~{Z},8~{Z})-tetradeca-1,3,5,8-tetraenyl]oxiran-2-yl]butanoic acid

Formula

C20 H30 O3

Formal charge

0

Molecular weight

318.45 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CCCCCC=CCC=CC=CC=C[CH]1O[CH]1CCCC(O)=O
SMILES OpenEye OEToolkits 2.0.6 CCCCCC=CCC=CC=CC=CC1C(O1)CCCC(=O)O
Canonical SMILES CACTVS 3.385 CCCCC/C=C\C\C=C/C=C/C=C/[C@@H]1O[C@H]1CCCC(O)=O
Canonical SMILES OpenEye OEToolkits 2.0.6 CCCCC/C=C\C/C=C\C=C\C=C\[C@H]1[C@@H](O1)CCCC(=O)O

IUPAC InChI

InChI=1S/C20H30O3/c1-2-3-4-5-6-7-8-9-10-11-12-13-15-18-19(23-18)16-14-17-20(21)22/h6-7,9-13,15,18-19H,2-5,8,14,16-17H2,1H3,(H,21,22)/b7-6-,10-9-,12-11+,15-13+/t18-,19-/m0/s1

IUPAC InChI key

UFPQIRYSPUYQHK-WAQVJNLQSA-N
DJ3

wwPDB Information

Atom count

53 (23 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2017-03-23

Last modified at

2019-09-04

Status

Released

Obsoleted

Not Assigned



DJ3 : Atoms of Molecule

Total Number of Atoms: 53
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 OAB O O1 N N N 0 -7.901 1.704 -1.495
2 CAU C C1 N N N 0 -7.638 2.355 -0.512
3 OAC O O2 N N N 0 -8.305 3.492 -0.262
4 CAR C C2 N N N 0 -6.566 1.885 0.438
5 CAQ C C3 N N N 0 -5.973 0.57 -0.072
6 CAS C C4 N N N 0 -4.885 0.094 0.891
7 CAW C C5 S N N 0 -4.292 -1.221 0.382
8 OAT O O3 N N N 0 -4.412 -2.374 1.217
9 CAV C C6 S N N 0 -3.102 -1.809 1.143
10 CAK C C7 N N N 0 -2.06 -2.555 0.349
11 CAG C C8 N N N 0 -0.795 -2.133 0.348
12 CAE C C9 N N N 0 0.217 -2.858 -0.423
13 CAD C C10 N N N 0 1.497 -2.432 -0.424
14 CAF C C11 N N N 0 2.51 -3.156 -1.195
15 CAH C C12 N N N 0 3.755 -2.685 -1.268
16 CAM C C13 N N N 0 4.16 -1.494 -0.439
17 CAI C C14 N N N 0 5.371 -1.845 0.387
18 CAJ C C15 N N N 0 6.433 -1.079 0.35
19 CAN C C16 N N N 0 6.392 0.231 -0.392
20 CAP C C17 N N N 0 6.844 1.359 0.539
21 CAO C C18 N N N 0 6.801 2.69 -0.215
22 CAL C C19 N N N 0 7.253 3.817 0.716
23 CAA C C20 N N N 0 7.211 5.148 -0.037
24 H1 H H1 N N N 0 -8.987 3.75 -0.897
25 HAY H H2 N N N 0 -5.781 2.638 0.499
26 HAX H H3 N N N 0 -6.999 1.73 1.426
27 HAV H H4 N N N 0 -6.759 -0.183 -0.134
28 HAW H H5 N N N 0 -5.541 0.726 -1.061
29 HAZ H H6 N N N 0 -4.099 0.847 0.953
30 HA0 H H7 N N N 0 -5.317 -0.062 1.88
31 HA2 H H8 N N N 0 -4.328 -1.369 -0.698
32 HA1 H H9 N N N 0 -2.734 -1.263 2.011
33 HAK H H10 N N N 0 -2.338 -3.43 -0.219
34 HAG H H11 N N N 0 -0.517 -1.258 0.916
35 HAE H H12 N N N 0 -0.06 -3.733 -0.991
36 HAD H H13 N N N 0 1.775 -1.556 0.144
37 HAF H H14 N N N 0 2.248 -4.072 -1.705
38 HAH H H15 N N N 0 4.473 -3.158 -1.922
39 HAN H H16 N N N 0 4.398 -0.658 -1.096
40 HAO H H17 N N N 0 3.339 -1.215 0.221
41 HAI H H18 N N N 0 5.363 -2.728 1.009
42 HAJ H H19 N N N 0 7.339 -1.388 0.852
43 HAP H H20 N N N 0 7.058 0.183 -1.253
44 HAQ H H21 N N N 0 5.374 0.426 -0.73
45 HAT H H22 N N N 0 6.178 1.408 1.4
46 HAU H H23 N N N 0 7.861 1.165 0.877
47 HAS H H24 N N N 0 7.468 2.641 -1.076
48 HAR H H25 N N N 0 5.784 2.884 -0.553
49 HAM H H26 N N N 0 6.588 3.866 1.577
50 HAL H H27 N N N 0 8.271 3.623 1.054
51 HAC H H28 N N N 0 6.194 5.342 -0.376
52 HAB H H29 N N N 0 7.533 5.951 0.626
53 HAA H H30 N N N 0 7.877 5.099 -0.899



DJ3 : 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 OAB CAU O C doub 1.21 N N
2 CAU OAC C O sing 1.34 N N
3 CAU CAR C C sing 1.51 N N
4 CAR CAQ C C sing 1.53 N N
5 CAQ CAS C C sing 1.53 N N
6 CAS CAW C C sing 1.53 N N
7 CAF CAH C C doub 1.33 Z N
8 CAF CAD C C sing 1.46 N N
9 CAE CAD C C doub 1.35 E N
10 CAE CAG C C sing 1.46 N N
11 CAK CAG C C doub 1.33 E N
12 CAK CAV C C sing 1.51 N N
13 CAW CAV C C sing 1.53 N N
14 CAW OAT C O sing 1.43 N N
15 CAH CAM C C sing 1.51 N N
16 CAV OAT C O sing 1.43 N N
17 CAM CAI C C sing 1.51 N N
18 CAI CAJ C C doub 1.31 Z N
19 CAN CAJ C C sing 1.51 N N
20 CAN CAP C C sing 1.53 N N
21 CAO CAP C C sing 1.53 N N
22 CAO CAL C C sing 1.53 N N
23 CAL CAA C C sing 1.53 N N
24 OAC H1 O H sing 0.97 N N
25 CAR HAY C H sing 1.09 N N
26 CAR HAX C H sing 1.09 N N
27 CAQ HAV C H sing 1.09 N N
28 CAQ HAW C H sing 1.09 N N
29 CAS HAZ C H sing 1.09 N N
30 CAS HA0 C H sing 1.09 N N
31 CAW HA2 C H sing 1.09 N N
32 CAV HA1 C H sing 1.09 N N
33 CAK HAK C H sing 1.08 N N
34 CAG HAG C H sing 1.08 N N
35 CAE HAE C H sing 1.08 N N
36 CAD HAD C H sing 1.08 N N
37 CAF HAF C H sing 1.08 N N
38 CAH HAH C H sing 1.08 N N
39 CAM HAN C H sing 1.09 N N
40 CAM HAO C H sing 1.09 N N
41 CAI HAI C H sing 1.08 N N
42 CAJ HAJ C H sing 1.08 N N
43 CAN HAP C H sing 1.09 N N
44 CAN HAQ C H sing 1.09 N N
45 CAP HAT C H sing 1.09 N N
46 CAP HAU C H sing 1.09 N N
47 CAO HAS C H sing 1.09 N N
48 CAO HAR C H sing 1.09 N N
49 CAL HAM C H sing 1.09 N N
50 CAL HAL C H sing 1.09 N N
51 CAA HAC C H sing 1.09 N N
52 CAA HAB C H sing 1.09 N N
53 CAA HAA C H sing 1.09 N N



DJ3 : Used in PDB Entries

Total Number of PDB Entries: 3
Ligand Code PDB Entry ID Type Total Distinct
DJ3 5ni2 Open in New Window Bound ligand 1 1
DJ3 5ni4 Open in New Window Bound ligand 3 1
DJ3 5ni6 Open in New Window Bound ligand 1 1