Chemical Components in the PDB

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LZZ : Summary

Code

LZZ

One-letter code

X

Molecule name

(3alpha,8alpha)-3,17-dihydroxypregn-5-en-20-one

Synonyms

17-Hydroxypregnenolone

Systematic names

ProgramVersionName
ACDLabs 12.01 (3alpha,8alpha)-3,17-dihydroxypregn-5-en-20-one
OpenEye OEToolkits 1.7.6 1-[(3S,8R,9S,10R,13S,14S,17R)-10,13-dimethyl-3,17-bis(oxidanyl)-1,2,3,4,7,8,9,11,12,14,15,16-dodecahydrocyclopenta[a]phenanthren-17-yl]ethanone

Formula

C21 H32 O3

Formal charge

0

Molecular weight

332.477 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(C4(O)C3(C(C1C(C2(C(=CC1)CC(O)CC2)C)CC3)CC4)C)C
SMILES CACTVS 3.385 CC(=O)[C]1(O)CC[CH]2[CH]3CC=C4C[CH](O)CC[C]4(C)[CH]3CC[C]12C
SMILES OpenEye OEToolkits 1.7.6 CC(=O)C1(CCC2C1(CCC3C2CC=C4C3(CCC(C4)O)C)C)O
Canonical SMILES CACTVS 3.385 CC(=O)[C@@]1(O)CC[C@H]2[C@@H]3CC=C4C[C@@H](O)CC[C@]4(C)[C@H]3CC[C@]12C
Canonical SMILES OpenEye OEToolkits 1.7.6 CC(=O)[C@]1(CC[C@@H]2[C@@]1(CC[C@H]3[C@H]2CC=C4[C@@]3(CC[C@@H](C4)O)C)C)O

IUPAC InChI

InChI=1S/C21H32O3/c1-13(22)21(24)11-8-18-16-5-4-14-12-15(23)6-9-19(14,2)17(16)7-10-20(18,21)3/h4,15-18,23-24H,5-12H2,1-3H3/t15-,16+,17-,18-,19-,20-,21-/m0/s1

IUPAC InChI key

JERGUCIJOXJXHF-TVWVXWENSA-N
LZZ

wwPDB Information

Atom count

56 (24 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2013-11-15

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



LZZ : Atoms of Molecule

Total Number of Atoms: 56
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 CAA C CAA N N N 0 -3.023 -1.318 0.919
2 CAB C CAB N N N 0 -4.428 -1.469 0.332
3 CAC C CAC S N N 0 -5.104 -0.099 0.253
4 CAE C CAE N N N 0 -4.327 0.8 -0.714
5 CAF C CAF N N N 0 -2.878 0.853 -0.258
6 CAG C CAG N N N 0 -2.322 2.018 -0.105
7 CAH C CAH N N N 0 -0.901 2.192 0.347
8 CAI C CAI R N N 0 -0.099 0.949 -0.058
9 CAJ C CAJ S N N 0 1.306 1.046 0.55
10 CAK C CAK N N N 0 2.187 2.182 0.018
11 CAL C CAL N N N 0 3.624 1.685 0.333
12 CAM C CAM R N N 0 3.532 0.121 0.424
13 CAN C CAN N N N 0 4.461 -0.53 -0.567
14 CAP C CAP N N N 0 4.904 -1.956 -0.361
15 CAQ C CAQ S N N 0 2.082 -0.217 0.09
16 CAR C CAR N N N 0 1.926 -0.401 -1.42
17 CAS C CAS N N N 0 1.481 -1.405 0.818
18 CAT C CAT N N N 0 0.033 -1.552 0.325
19 CAU C CAU S N N 0 -0.777 -0.28 0.56
20 CAV C CAV R N N 0 -2.174 -0.449 -0.013
21 CAW C CAW N N N 0 -2.055 -1.17 -1.357
22 HA0 H HA0 N N N 0 -0.864 -0.122 1.635
23 HA1 H HA1 N N N 0 -1.44 -0.577 -2.034
24 HA2 H HA2 N N N 0 -1.591 -2.145 -1.207
25 HA3 H HA3 N N N 0 -3.047 -1.302 -1.788
26 HA4 H HA4 N N N 0 -6.935 0.575 -0.291
27 HA5 H HA5 N N N 0 4.756 -0.114 2.02
28 HAA H HAA N N N 0 -3.087 -0.845 1.899
29 HAB H HAB N N N 0 -2.564 -2.301 1.019
30 HAC H HAC N N N 0 -4.359 -1.897 -0.668
31 HAD H HAD N N N 0 -5.019 -2.127 0.968
32 HAE H HAE N N N 0 -5.117 0.357 1.243
33 HAF H HAF N N N 0 -4.752 1.804 -0.704
34 HAG H HAG N N N 0 -4.38 0.388 -1.721
35 HAH H HAH N N N 0 -2.91 2.901 -0.309
36 HAI H HAI N N N 0 -0.472 3.073 -0.13
37 HAJ H HAJ N N N 0 -0.876 2.315 1.43
38 HAK H HAK N N N 0 -0.043 0.875 -1.144
39 HAL H HAL N N N 0 1.246 1.078 1.638
40 HAM H HAM N N N 0 1.975 3.11 0.549
41 HAN H HAN N N N 0 2.05 2.311 -1.056
42 HAO H HAO N N N 0 4.304 1.973 -0.469
43 HAP H HAP N N N 0 3.965 2.102 1.281
44 HAQ H HAQ N N N 0 4.589 -2.561 -1.211
45 HAR H HAR N N N 0 4.453 -2.348 0.551
46 HAS H HAS N N N 0 5.99 -1.99 -0.273
47 HAT H HAT N N N 0 2.308 0.481 -1.935
48 HAU H HAU N N N 0 2.487 -1.279 -1.739
49 HAV H HAV N N N 0 0.872 -0.535 -1.663
50 HAW H HAW N N N 0 1.492 -1.226 1.893
51 HAX H HAX N N N 0 2.046 -2.307 0.586
52 HAY H HAY N N N 0 0.042 -1.776 -0.742
53 HAZ H HAZ N N N 0 -0.441 -2.377 0.857
54 OAD O OAD N N N 0 -6.445 -0.256 -0.216
55 OAO O OAO N N N 0 4.851 0.09 -1.528
56 OAX O OAX N N N 0 3.846 -0.303 1.752



LZZ : Chemical Bonds

Total Number of Bonds: 59
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 CAE CAF C C sing 1.52 N N
2 CAE CAC C C sing 1.53 N N
3 CAG CAH C C sing 1.5 N N
4 CAG CAF C C doub 1.3 N N
5 CAH CAI C C sing 1.53 N N
6 CAF CAV C C sing 1.5 N N
7 CAW CAV C C sing 1.53 N N
8 CAK CAL C C sing 1.55 N N
9 CAK CAJ C C sing 1.53 N N
10 OAD CAC O C sing 1.43 N N
11 CAI CAJ C C sing 1.53 N N
12 CAI CAU C C sing 1.53 N N
13 CAC CAB C C sing 1.53 N N
14 CAV CAU C C sing 1.52 N N
15 CAV CAA C C sing 1.53 N N
16 CAL CAM C C sing 1.57 N N
17 CAR CAQ C C sing 1.53 N N
18 CAJ CAQ C C sing 1.55 N N
19 CAB CAA C C sing 1.53 N N
20 CAU CAT C C sing 1.53 N N
21 CAQ CAM C C sing 1.53 N N
22 CAQ CAS C C sing 1.52 N N
23 CAT CAS C C sing 1.54 N N
24 CAM CAN C C sing 1.51 N N
25 CAM OAX C O sing 1.43 N N
26 OAO CAN O C doub 1.21 N N
27 CAN CAP C C sing 1.51 N N
28 CAR HAU C H sing 1.09 N N
29 CAR HAV C H sing 1.09 N N
30 CAR HAT C H sing 1.09 N N
31 CAS HAX C H sing 1.09 N N
32 CAS HAW C H sing 1.09 N N
33 CAT HAY C H sing 1.09 N N
34 CAT HAZ C H sing 1.09 N N
35 CAU HA0 C H sing 1.09 N N
36 CAW HA2 C H sing 1.09 N N
37 CAW HA3 C H sing 1.09 N N
38 CAW HA1 C H sing 1.09 N N
39 CAA HAB C H sing 1.09 N N
40 CAA HAA C H sing 1.09 N N
41 CAB HAC C H sing 1.09 N N
42 CAB HAD C H sing 1.09 N N
43 CAC HAE C H sing 1.09 N N
44 OAD HA4 O H sing 0.97 N N
45 CAE HAG C H sing 1.09 N N
46 CAE HAF C H sing 1.09 N N
47 CAG HAH C H sing 1.08 N N
48 CAH HAI C H sing 1.09 N N
49 CAH HAJ C H sing 1.09 N N
50 CAI HAK C H sing 1.09 N N
51 CAJ HAL C H sing 1.09 N N
52 CAK HAN C H sing 1.09 N N
53 CAK HAM C H sing 1.09 N N
54 CAL HAO C H sing 1.09 N N
55 CAL HAP C H sing 1.09 N N
56 OAX HA5 O H sing 0.97 N N
57 CAP HAR C H sing 1.09 N N
58 CAP HAQ C H sing 1.09 N N
59 CAP HAS C H sing 1.09 N N



LZZ : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
LZZ 4nkz Open in New Window Bound ligand 4 1