Chemical Components in the PDB

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HCY : Summary

Code

HCY

One-letter code

X

Molecule name

(11alpha,14beta)-11,17,21-trihydroxypregn-4-ene-3,20-dione

Synonyms

CORTISOL

Systematic names

ProgramVersionName
ACDLabs 10.04 (11alpha,14beta)-11,17,21-trihydroxypregn-4-ene-3,20-dione
OpenEye OEToolkits 1.5.0 (8S,9S,10R,11S,13S,14S,17R)-11,17-dihydroxy-17-(2-hydroxyethanoyl)-10,13-dimethyl-2,6,7,8,9,11,12,14,15,16-decahydro-1H-cyclopenta[a]phenanthren-3-one

Formula

C21 H30 O5

Formal charge

0

Molecular weight

362.46 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(CO)C3(O)C2(CC(O)C4C1(C(=CC(=O)CC1)CCC4C2CC3)C)C
SMILES CACTVS 3.341 C[C]12CCC(=O)C=C1CC[CH]3[CH]4CC[C](O)(C(=O)CO)[C]4(C)C[CH](O)[CH]23
SMILES OpenEye OEToolkits 1.5.0 CC12CCC(=O)C=C1CCC3C2C(CC4(C3CCC4(C(=O)CO)O)C)O
Canonical SMILES CACTVS 3.341 C[C@]12CCC(=O)C=C1CC[C@H]3[C@@H]4CC[C@](O)(C(=O)CO)[C@@]4(C)C[C@H](O)[C@H]23
Canonical SMILES OpenEye OEToolkits 1.5.0 C[C@]12CCC(=O)C=C1CC[C@@H]3[C@@H]2[C@H](C[C@]4([C@H]3CC[C@@]4(C(=O)CO)O)C)O

IUPAC InChI

InChI=1S/C21H30O5/c1-19-7-5-13(23)9-12(19)3-4-14-15-6-8-21(26,17(25)11-22)20(15,2)10-16(24)18(14)19/h9,14-16,18,22,24,26H,3-8,10-11H2,1-2H3/t14-,15-,16-,18+,19-,20-,21-/m0/s1

IUPAC InChI key

JYGXADMDTFJGBT-VWUMJDOOSA-N
HCY

wwPDB Information

Atom count

56 (26 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

Is modified

No

Standard parent

Not Assigned

Defined at

2007-10-13

Last modified at

2021-03-01

Status

Released

Obsoleted

Not Assigned



HCY : 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 C1 C C1 N N N 0 -3.163 1.695 -0.082
2 C2 C C2 N N N 0 -4.238 1.421 -1.133
3 C3 C C3 N N N 0 -5.209 0.415 -0.545
4 C4 C C4 N N N 0 -4.614 -0.816 -0.005
5 C5 C C5 N N N 0 -3.351 -0.794 0.41
6 C6 C C6 N N N 0 -2.725 -2.078 0.927
7 C7 C C7 N N N 0 -1.427 -2.309 0.145
8 C8 C C8 S N N 0 -0.52 -1.084 0.266
9 C9 C C9 S N N 0 -1.202 0.14 -0.37
10 C10 C C10 R N N 0 -2.491 0.432 0.397
11 C12 C C12 N N N 0 1.069 1.082 -0.981
12 C11 C C11 S N N 0 -0.296 1.367 -0.335
13 C13 C C13 S N N 0 1.684 -0.086 -0.234
14 C14 C C14 S N N 0 0.777 -1.321 -0.486
15 C15 C C15 N N N 0 1.654 -2.463 0.038
16 C16 C C16 N N N 0 3.066 -2.087 -0.488
17 C17 C C17 R N N 0 3.054 -0.554 -0.714
18 C18 C C18 N N N 0 1.734 0.224 1.263
19 C19 C C19 N N N 0 -2.068 0.683 1.846
20 C20 C C20 N N N 0 4.143 0.101 0.096
21 C21 C C21 N N N 0 4.679 1.449 -0.313
22 O1 O O1 N N N 0 -6.406 0.614 -0.521
23 O2 O O2 N N N 0 -0.097 1.761 1.024
24 O3 O O3 N N N 0 3.221 -0.257 -2.102
25 O4 O O4 N N N 0 4.586 -0.454 1.073
26 O5 O O5 N N N 0 5.696 1.856 0.605
27 H4 H H4 N N N 0 -5.194 -1.725 0.053
28 H2C1 H 1H2C N N N 0 -4.764 2.345 -1.374
29 H2C2 H 2H2C N N N 0 -3.78 1.011 -2.033
30 H6C1 H 1H6C N N N 0 -2.504 -1.981 1.99
31 H6C2 H 2H6C N N N 0 -3.407 -2.913 0.765
32 H7C1 H 1H7C N N N 0 -0.912 -3.181 0.547
33 H7C2 H 2H7C N N N 0 -1.662 -2.482 -0.905
34 H8 H H8 N N N 0 -0.304 -0.89 1.317
35 H1C1 H 1H1C N N N 0 -2.409 2.354 -0.512
36 H1C2 H 2H1C N N N 0 -3.624 2.194 0.77
37 H9 H H9 N N N 0 -1.458 -0.089 -1.405
38 H191 H 1H19 N N N 0 -2.927 0.553 2.503
39 H192 H 2H19 N N N 0 -1.287 -0.024 2.124
40 H193 H 3H19 N N N 0 -1.688 1.701 1.942
41 H121 H 1H12 N N N 0 0.937 0.823 -2.031
42 H11 H H11 N N N 0 -0.78 2.181 -0.874
43 H14 H H14 N N N 0 0.58 -1.438 -1.552
44 H2 H H2 N N N 0 0.47 2.537 1.129
45 H122 H 2H12 N N N 0 1.712 1.958 -0.893
46 H181 H 1H18 N N N 0 0.721 0.23 1.667
47 H182 H 2H18 N N N 0 2.323 -0.538 1.773
48 H183 H 3H18 N N N 0 2.192 1.201 1.417
49 H151 H 1H15 N N N 0 1.643 -2.489 1.128
50 H152 H 2H15 N N N 0 1.33 -3.418 -0.375
51 H161 H 1H16 N N N 0 3.823 -2.35 0.25
52 H162 H 2H16 N N N 0 3.264 -2.602 -1.428
53 H3 H H3 N N N 0 4.075 -0.532 -2.463
54 H211 H 1H21 N N N 0 5.1 1.383 -1.316
55 H212 H 2H21 N N N 0 3.87 2.179 -0.306
56 H5 H H5 N N N 0 6.087 2.717 0.403



HCY : 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 O1 C3 O C doub 1.21 N N
2 C3 C4 C C sing 1.47 N N
3 C3 C2 C C sing 1.52 N N
4 C4 C5 C C doub 1.33 N N
5 C5 C6 C C sing 1.52 N N
6 C5 C10 C C sing 1.5 N N
7 C6 C7 C C sing 1.53 N N
8 C7 C8 C C sing 1.53 N N
9 C2 C1 C C sing 1.53 N N
10 C1 C10 C C sing 1.51 N N
11 C10 C19 C C sing 1.53 N N
12 C10 C9 C C sing 1.53 N N
13 C9 C8 C C sing 1.54 N N
14 C9 C11 C C sing 1.53 N N
15 C8 C14 C C sing 1.52 N N
16 C11 O2 C O sing 1.43 N N
17 C11 C12 C C sing 1.54 N N
18 C12 C13 C C sing 1.52 N N
19 C13 C18 C C sing 1.53 N N
20 C13 C14 C C sing 1.55 N N
21 C13 C17 C C sing 1.53 N N
22 C14 C15 C C sing 1.53 N N
23 C15 C16 C C sing 1.55 N N
24 C16 C17 C C sing 1.55 N N
25 C17 O3 C O sing 1.43 N N
26 C17 C20 C C sing 1.51 N N
27 C20 O4 C O doub 1.21 N N
28 C20 C21 C C sing 1.51 N N
29 C21 O5 C O sing 1.43 N N
30 C4 H4 C H sing 1.08 N N
31 C2 H2C1 C H sing 1.09 N N
32 C2 H2C2 C H sing 1.09 N N
33 C6 H6C1 C H sing 1.09 N N
34 C6 H6C2 C H sing 1.09 N N
35 C7 H7C1 C H sing 1.09 N N
36 C7 H7C2 C H sing 1.09 N N
37 C8 H8 C H sing 1.09 N N
38 C1 H1C1 C H sing 1.09 N N
39 C1 H1C2 C H sing 1.09 N N
40 C19 H191 C H sing 1.09 N N
41 C19 H192 C H sing 1.09 N N
42 C19 H193 C H sing 1.09 N N
43 C9 H9 C H sing 1.09 N N
44 C11 H11 C H sing 1.09 N N
45 C14 H14 C H sing 1.09 N N
46 O2 H2 O H sing 0.97 N N
47 C12 H121 C H sing 1.09 N N
48 C12 H122 C H sing 1.09 N N
49 C18 H181 C H sing 1.09 N N
50 C18 H182 C H sing 1.09 N N
51 C18 H183 C H sing 1.09 N N
52 C15 H151 C H sing 1.09 N N
53 C15 H152 C H sing 1.09 N N
54 C16 H161 C H sing 1.09 N N
55 C16 H162 C H sing 1.09 N N
56 O3 H3 O H sing 0.97 N N
57 C21 H211 C H sing 1.09 N N
58 C21 H212 C H sing 1.09 N N
59 O5 H5 O H sing 0.97 N N



HCY : Used in PDB Entries

Total Number of PDB Entries: 12
Ligand Code PDB Entry ID Type Total Distinct
HCY 2v95 Open in New Window Bound ligand 1 1
HCY 2vdy Open in New Window Bound ligand 2 1
HCY 4c49 Open in New Window Bound ligand 4 1
HCY 4p6x Open in New Window Bound ligand 6 1
HCY 5hgc Open in New Window Bound ligand 1 1
HCY 6hgf Open in New Window Bound ligand 1 1
HCY 6hgg Open in New Window Bound ligand 1 1
HCY 6itp Open in New Window Bound ligand 2 1
HCY 6itq Open in New Window Bound ligand 4 1
HCY 6nwl Open in New Window Bound ligand 1 1
HCY 7d77 Open in New Window Bound ligand 1 1
HCY 8cby Open in New Window Bound ligand 1 1