Structure

Physi-Chem Properties

Molecular Weight:  328.17
Volume:  365.909
LogP:  1.366
LogD:  -0.291
LogS:  -3.694
# Rotatable Bonds:  8
TPSA:  74.6
# H-Bond Aceptor:  4
# H-Bond Donor:  2
# Rings:  0
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.504
Synthetic Accessibility Score:  3.35
Fsp3:  0.2
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.511
MDCK Permeability:  1.0963216482196003e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.006
Human Intestinal Absorption (HIA):  0.015
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.003

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.083
Plasma Protein Binding (PPB):  92.9220199584961%
Volume Distribution (VD):  0.565
Pgp-substrate:  5.7254815101623535%

ADMET: Metabolism

CYP1A2-inhibitor:  0.582
CYP1A2-substrate:  0.12
CYP2C19-inhibitor:  0.192
CYP2C19-substrate:  0.045
CYP2C9-inhibitor:  0.439
CYP2C9-substrate:  0.996
CYP2D6-inhibitor:  0.776
CYP2D6-substrate:  0.926
CYP3A4-inhibitor:  0.06
CYP3A4-substrate:  0.043

ADMET: Excretion

Clearance (CL):  0.744
Half-life (T1/2):  0.738

ADMET: Toxicity

hERG Blockers:  0.005
Human Hepatotoxicity (H-HT):  0.815
Drug-inuced Liver Injury (DILI):  0.913
AMES Toxicity:  0.007
Rat Oral Acute Toxicity:  0.377
Maximum Recommended Daily Dose:  0.026
Skin Sensitization:  0.74
Carcinogencity:  0.406
Eye Corrosion:  0.009
Eye Irritation:  0.837
Respiratory Toxicity:  0.549

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Data Type Select
General Info & Identifiers & Properties  
Structure MOL file  
Source Organisms  
Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC43053

Natural Product ID:  NPC43053
Common Name*:   Crocetin
IUPAC Name:   (2E,4E,6E,8E,10E,12E,14E)-2,6,11,15-tetramethylhexadeca-2,4,6,8,10,12,14-heptaenedioic acid
Synonyms:   Crocetin
Standard InCHIKey:  PANKHBYNKQNAHN-MQQNZMFNSA-N
Standard InCHI:  InChI=1S/C20H24O4/c1-15(11-7-13-17(3)19(21)22)9-5-6-10-16(2)12-8-14-18(4)20(23)24/h5-14H,1-4H3,(H,21,22)(H,23,24)/b6-5+,11-7+,12-8+,15-9+,16-10+,17-13+,18-14+
SMILES:  C/C(=CC=CC=C(C=CC=C(C(=O)O)/C)/C)/C=C/C=C(/C(=O)O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL464792
PubChem CID:   5281232
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001551] Diterpenoids
          • [CHEMONTID:0001357] Acyclic diterpenoids

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO9445 Crocus sativus Species Iridaceae Eukaryota n.a. n.a. n.a. DOI[10.1002/hlca.19270100148]
NPO9445 Crocus sativus Species Iridaceae Eukaryota Petals n.a. n.a. PMID[15043425]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota Fruits n.a. n.a. PMID[16309325]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. Seoul, Korea 2000-Jun PMID[16643034]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota fruit n.a. n.a. PMID[18505286]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota fruit n.a. n.a. PMID[19650637]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota fruits n.a. n.a. PMID[23305920]
NPO9445 Crocus sativus Species Iridaceae Eukaryota n.a. n.a. n.a. PMID[24338885]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. n.a. n.a. PMID[32141747]
NPO41841 A new engineered strain of Daldinia eschscholzii [n.a.] Strain n.a. Eukaryota n.a. n.a. n.a. PMID[35387230]
NPO9445 Crocus sativus Species Iridaceae Eukaryota Silk Stigma Style n.a. n.a. Database[FooDB]
NPO9445 Crocus sativus Species Iridaceae Eukaryota n.a. n.a. Database[FooDB]
NPO9445 Crocus sativus Species Iridaceae Eukaryota n.a. n.a. Database[FooDB]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9445 Crocus sativus Species Iridaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9445 Crocus sativus Species Iridaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9445 Crocus sativus Species Iridaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9445 Crocus sativus Species Iridaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9445 Crocus sativus Species Iridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]

☑ Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

  NP Quantity Composition/Concentration

Organism ID NP ID Organism Material Preparation Organism Part NP Quantity (Standard) NP Quantity (Minimum) NP Quantity (Maximum) Quantity Unit Reference

☑ Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

  Biological Activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT30 Individual Protein Cyclooxygenase-1 Homo sapiens IC50 = 28000.0 nM PMID[458274]
NPT113 Cell Line RAW264.7 Mus musculus IC50 = 5990.0 nM PMID[458275]
NPT2 Others Unspecified IC50 = 37500.0 nM PMID[458276]
NPT2 Others Unspecified IC20 = 2.52 10'-5M PMID[458276]
NPT21312 SINGLE PROTEIN Diacylglycerol O-acyltransferase 1 Bos taurus Inhibition = 15.0 % PMID[458276]
NPT21312 SINGLE PROTEIN Diacylglycerol O-acyltransferase 1 Bos taurus Inhibition = 34.0 % PMID[458276]
NPT21313 SINGLE PROTEIN Lecithin retinol acyltransferase Bos taurus Inhibition = 0.0 % PMID[458276]
NPT21313 SINGLE PROTEIN Lecithin retinol acyltransferase Bos taurus Inhibition = 15.0 % PMID[458276]
NPT2 Others Unspecified Activity = 90.0 % PMID[458276]

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

  Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

●  The left chart: Distribution of similarity level between NPC43053 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).

Similarity Score Similarity Level Natural Product ID
0.898 High Similarity NPC221467
0.8036 Intermediate Similarity NPC254095
0.8 Intermediate Similarity NPC308331
0.8 Intermediate Similarity NPC87137
0.7963 Intermediate Similarity NPC474127
0.7959 Intermediate Similarity NPC304079
0.7959 Intermediate Similarity NPC6963
0.7872 Intermediate Similarity NPC8270
0.7857 Intermediate Similarity NPC135863
0.7857 Intermediate Similarity NPC249850
0.7857 Intermediate Similarity NPC283502
0.7857 Intermediate Similarity NPC293437
0.7719 Intermediate Similarity NPC223679
0.7719 Intermediate Similarity NPC189700
0.7708 Intermediate Similarity NPC221250
0.7586 Intermediate Similarity NPC82465
0.7544 Intermediate Similarity NPC129150
0.7544 Intermediate Similarity NPC294938
0.7447 Intermediate Similarity NPC63598
0.7414 Intermediate Similarity NPC471619
0.7414 Intermediate Similarity NPC21946
0.7368 Intermediate Similarity NPC324224
0.7368 Intermediate Similarity NPC472808
0.7368 Intermediate Similarity NPC51846
0.7358 Intermediate Similarity NPC137419
0.7358 Intermediate Similarity NPC122212
0.7321 Intermediate Similarity NPC322461
0.7321 Intermediate Similarity NPC478120
0.7321 Intermediate Similarity NPC218486
0.7302 Intermediate Similarity NPC254886
0.7258 Intermediate Similarity NPC471566
0.7258 Intermediate Similarity NPC471565
0.7234 Intermediate Similarity NPC107877
0.7222 Intermediate Similarity NPC15789
0.7213 Intermediate Similarity NPC68110
0.72 Intermediate Similarity NPC102879
0.7167 Intermediate Similarity NPC130953
0.7167 Intermediate Similarity NPC98519
0.7143 Intermediate Similarity NPC308294
0.7143 Intermediate Similarity NPC142423
0.7077 Intermediate Similarity NPC236208
0.7069 Intermediate Similarity NPC325977
0.7069 Intermediate Similarity NPC221763
0.7069 Intermediate Similarity NPC150717
0.7059 Intermediate Similarity NPC270796
0.7049 Intermediate Similarity NPC317177
0.7049 Intermediate Similarity NPC317025
0.7049 Intermediate Similarity NPC326645
0.7049 Intermediate Similarity NPC329416
0.7021 Intermediate Similarity NPC308418
0.7015 Intermediate Similarity NPC238948
0.7015 Intermediate Similarity NPC12815
0.7015 Intermediate Similarity NPC215745
0.7 Intermediate Similarity NPC322186
0.6984 Remote Similarity NPC273600
0.6984 Remote Similarity NPC471556
0.6981 Remote Similarity NPC128280
0.697 Remote Similarity NPC59558
0.6964 Remote Similarity NPC191643
0.6935 Remote Similarity NPC2328
0.6935 Remote Similarity NPC322457
0.6935 Remote Similarity NPC473737
0.6935 Remote Similarity NPC77891
0.6909 Remote Similarity NPC236338
0.6897 Remote Similarity NPC173157
0.6897 Remote Similarity NPC478117
0.6875 Remote Similarity NPC146811
0.6866 Remote Similarity NPC316185
0.6833 Remote Similarity NPC34416
0.6833 Remote Similarity NPC474084
0.6818 Remote Similarity NPC143396
0.6809 Remote Similarity NPC297363
0.6809 Remote Similarity NPC60675
0.6792 Remote Similarity NPC270706
0.6792 Remote Similarity NPC117572
0.6786 Remote Similarity NPC15129
0.6774 Remote Similarity NPC40082
0.6774 Remote Similarity NPC26810
0.6727 Remote Similarity NPC267110
0.6721 Remote Similarity NPC329249
0.6721 Remote Similarity NPC86789
0.6721 Remote Similarity NPC329550
0.6721 Remote Similarity NPC322002
0.6721 Remote Similarity NPC318306
0.6719 Remote Similarity NPC7940
0.6714 Remote Similarity NPC4492
0.6714 Remote Similarity NPC51391
0.6667 Remote Similarity NPC268185
0.6667 Remote Similarity NPC472445
0.6667 Remote Similarity NPC179087
0.6667 Remote Similarity NPC71755
0.6667 Remote Similarity NPC44343
0.6667 Remote Similarity NPC315843
0.6667 Remote Similarity NPC227396
0.6667 Remote Similarity NPC210303
0.6618 Remote Similarity NPC293114
0.6615 Remote Similarity NPC475675
0.6615 Remote Similarity NPC475555
0.6615 Remote Similarity NPC255781
0.6613 Remote Similarity NPC251042
0.6613 Remote Similarity NPC122521
0.6613 Remote Similarity NPC174447
0.6613 Remote Similarity NPC327112
0.6613 Remote Similarity NPC309408
0.6613 Remote Similarity NPC328311
0.6604 Remote Similarity NPC138935
0.6596 Remote Similarity NPC224651
0.6596 Remote Similarity NPC217161
0.6596 Remote Similarity NPC98098
0.6545 Remote Similarity NPC91495
0.6522 Remote Similarity NPC284006
0.6508 Remote Similarity NPC263732
0.6508 Remote Similarity NPC55376
0.6508 Remote Similarity NPC64985
0.6491 Remote Similarity NPC48162
0.6491 Remote Similarity NPC178586
0.6481 Remote Similarity NPC160628
0.6471 Remote Similarity NPC476037
0.6471 Remote Similarity NPC315597
0.6462 Remote Similarity NPC282760
0.6452 Remote Similarity NPC97570
0.6441 Remote Similarity NPC189677
0.6441 Remote Similarity NPC300121
0.6441 Remote Similarity NPC154626
0.6438 Remote Similarity NPC63326
0.6438 Remote Similarity NPC265980
0.6429 Remote Similarity NPC149821
0.6429 Remote Similarity NPC313553
0.6429 Remote Similarity NPC234084
0.6429 Remote Similarity NPC5413
0.6429 Remote Similarity NPC126184
0.6429 Remote Similarity NPC107654
0.6418 Remote Similarity NPC474823
0.6415 Remote Similarity NPC116934
0.6406 Remote Similarity NPC190049
0.6406 Remote Similarity NPC155849
0.6393 Remote Similarity NPC44542
0.6393 Remote Similarity NPC245650
0.6379 Remote Similarity NPC229046
0.6379 Remote Similarity NPC46565
0.6377 Remote Similarity NPC288667
0.6377 Remote Similarity NPC319163
0.6377 Remote Similarity NPC67076
0.6364 Remote Similarity NPC315115
0.6364 Remote Similarity NPC42304
0.6364 Remote Similarity NPC197467
0.6364 Remote Similarity NPC81907
0.6349 Remote Similarity NPC305973
0.6349 Remote Similarity NPC79756
0.6338 Remote Similarity NPC260396
0.6338 Remote Similarity NPC478195
0.6338 Remote Similarity NPC478192
0.6338 Remote Similarity NPC478196
0.6338 Remote Similarity NPC68624
0.6338 Remote Similarity NPC478193
0.6338 Remote Similarity NPC478194
0.6338 Remote Similarity NPC169056
0.6338 Remote Similarity NPC166018
0.6338 Remote Similarity NPC225665
0.6338 Remote Similarity NPC478191
0.6324 Remote Similarity NPC151481
0.6324 Remote Similarity NPC475004
0.6316 Remote Similarity NPC225974
0.6316 Remote Similarity NPC59051
0.6296 Remote Similarity NPC477686
0.6286 Remote Similarity NPC329890
0.6286 Remote Similarity NPC316851
0.6275 Remote Similarity NPC298413
0.6271 Remote Similarity NPC61177
0.6269 Remote Similarity NPC132286
0.6269 Remote Similarity NPC49863
0.6269 Remote Similarity NPC122627
0.6269 Remote Similarity NPC225272
0.625 Remote Similarity NPC203277
0.625 Remote Similarity NPC273614
0.625 Remote Similarity NPC470705
0.625 Remote Similarity NPC128520
0.625 Remote Similarity NPC207292
0.6232 Remote Similarity NPC67183
0.6232 Remote Similarity NPC476012
0.6232 Remote Similarity NPC315285
0.623 Remote Similarity NPC18951
0.6226 Remote Similarity NPC41409
0.6226 Remote Similarity NPC169098
0.6226 Remote Similarity NPC187922
0.6212 Remote Similarity NPC317881
0.6212 Remote Similarity NPC255863
0.6212 Remote Similarity NPC19769
0.6212 Remote Similarity NPC96414
0.6212 Remote Similarity NPC320642
0.6212 Remote Similarity NPC323477
0.6212 Remote Similarity NPC245947
0.6212 Remote Similarity NPC323045
0.6212 Remote Similarity NPC318420
0.6212 Remote Similarity NPC326268
0.6212 Remote Similarity NPC136164
0.6207 Remote Similarity NPC477777
0.6207 Remote Similarity NPC284212
0.6197 Remote Similarity NPC470686
0.619 Remote Similarity NPC106851

  Chemically structural similarity: II. Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

●  The left chart: Distribution of similarity level between NPC43053 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
0.8776 High Similarity NPD4220 Pre-registration
0.7755 Intermediate Similarity NPD9411 Phase 1
0.7059 Intermediate Similarity NPD5326 Phase 3
0.7049 Intermediate Similarity NPD4194 Approved
0.7049 Intermediate Similarity NPD4191 Approved
0.7049 Intermediate Similarity NPD4192 Approved
0.7049 Intermediate Similarity NPD4193 Approved
0.6792 Remote Similarity NPD4222 Approved
0.6792 Remote Similarity NPD39 Approved
0.6613 Remote Similarity NPD4246 Clinical (unspecified phase)
0.6596 Remote Similarity NPD8573 Approved
0.6429 Remote Similarity NPD3173 Approved
0.6389 Remote Similarity NPD4756 Discovery
0.6269 Remote Similarity NPD4247 Clinical (unspecified phase)
0.6207 Remote Similarity NPD6927 Phase 3
0.6182 Remote Similarity NPD4265 Approved
0.6 Remote Similarity NPD3172 Approved
0.6 Remote Similarity NPD6096 Approved
0.6 Remote Similarity NPD6097 Approved
0.5957 Remote Similarity NPD9114 Clinical (unspecified phase)
0.5902 Remote Similarity NPD3194 Approved
0.5902 Remote Similarity NPD3196 Approved
0.5902 Remote Similarity NPD4266 Approved
0.5902 Remote Similarity NPD3195 Phase 2
0.5893 Remote Similarity NPD3174 Discontinued
0.5882 Remote Similarity NPD9115 Approved
0.569 Remote Similarity NPD5343 Approved
0.566 Remote Similarity NPD5783 Phase 3
0.5645 Remote Similarity NPD539 Approved

  Bioactivity similarity: Similar Natural Products in NPASS

Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.

Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity
B: biological targets similarity
C: networks similarity
D: cell-based bioactivity similarity
E: similarity based on clinical data