Structure

Physi-Chem Properties

Molecular Weight:  656.55
Volume:  792.751
LogP:  11.349
LogD:  5.022
LogS:  -1.875
# Rotatable Bonds:  32
TPSA:  40.46
# H-Bond Aceptor:  2
# H-Bond Donor:  2
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.043
Synthetic Accessibility Score:  4.218
Fsp3:  0.696
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.181
MDCK Permeability:  7.4330359893792775e-06
Pgp-inhibitor:  0.0
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.924
20% Bioavailability (F20%):  0.968
30% Bioavailability (F30%):  0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.003
Plasma Protein Binding (PPB):  107.33055877685547%
Volume Distribution (VD):  1.664
Pgp-substrate:  0.2777352035045624%

ADMET: Metabolism

CYP1A2-inhibitor:  0.069
CYP1A2-substrate:  0.107
CYP2C19-inhibitor:  0.549
CYP2C19-substrate:  0.056
CYP2C9-inhibitor:  0.092
CYP2C9-substrate:  0.998
CYP2D6-inhibitor:  0.03
CYP2D6-substrate:  0.014
CYP3A4-inhibitor:  0.35
CYP3A4-substrate:  0.036

ADMET: Excretion

Clearance (CL):  4.101
Half-life (T1/2):  0.249

ADMET: Toxicity

hERG Blockers:  0.021
Human Hepatotoxicity (H-HT):  0.256
Drug-inuced Liver Injury (DILI):  0.67
AMES Toxicity:  0.161
Rat Oral Acute Toxicity:  0.942
Maximum Recommended Daily Dose:  1.0
Skin Sensitization:  0.994
Carcinogencity:  0.096
Eye Corrosion:  0.865
Eye Irritation:  0.947
Respiratory Toxicity:  0.982

Download Data

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

  Natural Product: NPC26102

Natural Product ID:  NPC26102
Common Name*:   Petrocortyne D
IUPAC Name:   (3S,14R,21Z,27Z,43Z)-hexatetraconta-21,27,43-trien-1,12,15,45-tetrayne-3,14-diol
Synonyms:   Petrocortyne D
Standard InCHIKey:  WZGVLTCUKBJJMW-MBQJZNLDSA-N
Standard InCHI:  InChI=1S/C46H72O2/c1-3-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20-21-22-23-24-25-26-27-28-29-30-34-37-40-43-46(48)44-41-38-35-32-31-33-36-39-42-45(47)4-2/h1-2,5-6,21-22,27-28,45-48H,7-20,23-26,29-39,42H2/b6-5-,22-21-,28-27-/t45-,46+/m1/s1
SMILES:  C#C/C=CCCCCCCCCCCCCCC/C=CCCCC/C=CCCCCC#C[C@@H](C#CCCCCCCCC[C@@H](C#C)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL442617
PubChem CID:   10508518
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0001334] Fatty alcohols

*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
NPO30927 Petrosia Genus Petrosiidae Eukaryota n.a. n.a. n.a. PMID[10514299]
NPO30927 Petrosia Genus Petrosiidae Eukaryota n.a. n.a. n.a. PMID[21534590]
NPO30927 Petrosia Genus Petrosiidae Eukaryota n.a. n.a. n.a. PMID[9784165]

☑ 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
NPT111 Cell Line K562 Homo sapiens LC50 = 45000.0 nM PMID[464268]

☑ 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 NPC26102 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
1.0 High Similarity NPC477724
1.0 High Similarity NPC187361
0.9423 High Similarity NPC477661
0.9423 High Similarity NPC473847
0.9423 High Similarity NPC470968
0.9423 High Similarity NPC475384
0.9423 High Similarity NPC161838
0.9423 High Similarity NPC470966
0.9423 High Similarity NPC471960
0.9423 High Similarity NPC470967
0.9423 High Similarity NPC470969
0.9245 High Similarity NPC470970
0.9231 High Similarity NPC473896
0.9231 High Similarity NPC477725
0.9231 High Similarity NPC477726
0.9231 High Similarity NPC473910
0.9231 High Similarity NPC475353
0.9231 High Similarity NPC473735
0.9231 High Similarity NPC473725
0.9231 High Similarity NPC473721
0.9038 High Similarity NPC473532
0.8679 High Similarity NPC49059
0.8679 High Similarity NPC256209
0.8462 Intermediate Similarity NPC256656
0.8462 Intermediate Similarity NPC294278
0.8462 Intermediate Similarity NPC475477
0.8462 Intermediate Similarity NPC224148
0.8462 Intermediate Similarity NPC329608
0.8462 Intermediate Similarity NPC471959
0.8462 Intermediate Similarity NPC477723
0.8462 Intermediate Similarity NPC89824
0.8462 Intermediate Similarity NPC76198
0.8462 Intermediate Similarity NPC170776
0.8462 Intermediate Similarity NPC197272
0.8462 Intermediate Similarity NPC9273
0.8462 Intermediate Similarity NPC129263
0.8462 Intermediate Similarity NPC165447
0.8448 Intermediate Similarity NPC470965
0.8276 Intermediate Similarity NPC475984
0.8269 Intermediate Similarity NPC471281
0.8269 Intermediate Similarity NPC477727
0.8269 Intermediate Similarity NPC199286
0.82 Intermediate Similarity NPC76976
0.8148 Intermediate Similarity NPC34577
0.8113 Intermediate Similarity NPC55383
0.8113 Intermediate Similarity NPC151782
0.8077 Intermediate Similarity NPC471276
0.8077 Intermediate Similarity NPC302310
0.8077 Intermediate Similarity NPC125122
0.8077 Intermediate Similarity NPC471275
0.8077 Intermediate Similarity NPC471280
0.8039 Intermediate Similarity NPC157096
0.8 Intermediate Similarity NPC110732
0.8 Intermediate Similarity NPC108195
0.8 Intermediate Similarity NPC48058
0.7959 Intermediate Similarity NPC149668
0.7925 Intermediate Similarity NPC473913
0.7925 Intermediate Similarity NPC72699
0.7925 Intermediate Similarity NPC474642
0.7925 Intermediate Similarity NPC249670
0.78 Intermediate Similarity NPC252978
0.7736 Intermediate Similarity NPC31194
0.7736 Intermediate Similarity NPC248884
0.7736 Intermediate Similarity NPC153538
0.7736 Intermediate Similarity NPC85079
0.7719 Intermediate Similarity NPC470964
0.7719 Intermediate Similarity NPC311648
0.7692 Intermediate Similarity NPC124183
0.7692 Intermediate Similarity NPC35141
0.7692 Intermediate Similarity NPC19834
0.7692 Intermediate Similarity NPC55063
0.7647 Intermediate Similarity NPC101616
0.7619 Intermediate Similarity NPC473752
0.7586 Intermediate Similarity NPC48968
0.7586 Intermediate Similarity NPC594
0.7551 Intermediate Similarity NPC329762
0.7551 Intermediate Similarity NPC27444
0.7551 Intermediate Similarity NPC103236
0.7544 Intermediate Similarity NPC152668
0.7544 Intermediate Similarity NPC474513
0.7544 Intermediate Similarity NPC470963
0.7544 Intermediate Similarity NPC146551
0.7541 Intermediate Similarity NPC29697
0.75 Intermediate Similarity NPC276825
0.75 Intermediate Similarity NPC474496
0.7455 Intermediate Similarity NPC93639
0.7455 Intermediate Similarity NPC59408
0.7455 Intermediate Similarity NPC473672
0.7455 Intermediate Similarity NPC71053
0.7455 Intermediate Similarity NPC474495
0.7377 Intermediate Similarity NPC66460
0.7377 Intermediate Similarity NPC325929
0.7377 Intermediate Similarity NPC271282
0.7347 Intermediate Similarity NPC471282
0.7333 Intermediate Similarity NPC473652
0.7273 Intermediate Similarity NPC473768
0.7273 Intermediate Similarity NPC328784
0.7273 Intermediate Similarity NPC291437
0.7241 Intermediate Similarity NPC471239
0.7241 Intermediate Similarity NPC474644
0.7213 Intermediate Similarity NPC243532
0.7193 Intermediate Similarity NPC284224
0.717 Intermediate Similarity NPC269074
0.7167 Intermediate Similarity NPC469373
0.7143 Intermediate Similarity NPC226592
0.7143 Intermediate Similarity NPC470320
0.7119 Intermediate Similarity NPC473865
0.7119 Intermediate Similarity NPC474643
0.7097 Intermediate Similarity NPC477829
0.7097 Intermediate Similarity NPC168407
0.7097 Intermediate Similarity NPC321838
0.7097 Intermediate Similarity NPC201939
0.7091 Intermediate Similarity NPC475153
0.7049 Intermediate Similarity NPC122239
0.7018 Intermediate Similarity NPC142092
0.7018 Intermediate Similarity NPC473705
0.7 Intermediate Similarity NPC52012
0.7 Intermediate Similarity NPC193975
0.7 Intermediate Similarity NPC474577
0.6949 Remote Similarity NPC54766
0.6949 Remote Similarity NPC52264
0.6949 Remote Similarity NPC281590
0.6939 Remote Similarity NPC216416
0.6935 Remote Similarity NPC471278
0.6923 Remote Similarity NPC249801
0.6923 Remote Similarity NPC46248
0.6909 Remote Similarity NPC471958
0.6885 Remote Similarity NPC226848
0.6842 Remote Similarity NPC29234
0.6833 Remote Similarity NPC187777
0.6833 Remote Similarity NPC179764
0.6825 Remote Similarity NPC328776
0.6825 Remote Similarity NPC475251
0.6825 Remote Similarity NPC320305
0.68 Remote Similarity NPC34873
0.68 Remote Similarity NPC40434
0.6786 Remote Similarity NPC98284
0.678 Remote Similarity NPC137538
0.6774 Remote Similarity NPC474267
0.6774 Remote Similarity NPC326524
0.6774 Remote Similarity NPC329003
0.6774 Remote Similarity NPC325550
0.6769 Remote Similarity NPC245947
0.6769 Remote Similarity NPC255863
0.6769 Remote Similarity NPC136164
0.6769 Remote Similarity NPC308844
0.6735 Remote Similarity NPC213767
0.6727 Remote Similarity NPC180575
0.6716 Remote Similarity NPC48218
0.6716 Remote Similarity NPC473559
0.6716 Remote Similarity NPC141481
0.6716 Remote Similarity NPC324981
0.6667 Remote Similarity NPC473487
0.6667 Remote Similarity NPC473863
0.6667 Remote Similarity NPC227135
0.6667 Remote Similarity NPC317899
0.6667 Remote Similarity NPC327112
0.6667 Remote Similarity NPC274290
0.6667 Remote Similarity NPC288381
0.6667 Remote Similarity NPC113224
0.6667 Remote Similarity NPC20934
0.6618 Remote Similarity NPC291196
0.6618 Remote Similarity NPC103712
0.6615 Remote Similarity NPC68343
0.6615 Remote Similarity NPC328089
0.6613 Remote Similarity NPC321030
0.661 Remote Similarity NPC217188
0.6604 Remote Similarity NPC304151
0.6567 Remote Similarity NPC330426
0.6567 Remote Similarity NPC473829
0.6567 Remote Similarity NPC104537
0.6567 Remote Similarity NPC271921
0.6567 Remote Similarity NPC26500
0.6567 Remote Similarity NPC99619
0.6567 Remote Similarity NPC148192
0.6567 Remote Similarity NPC475443
0.6567 Remote Similarity NPC22101
0.6567 Remote Similarity NPC127091
0.6557 Remote Similarity NPC477201
0.6545 Remote Similarity NPC140501
0.6522 Remote Similarity NPC476660
0.6515 Remote Similarity NPC318420
0.6515 Remote Similarity NPC326268
0.6508 Remote Similarity NPC473866
0.6508 Remote Similarity NPC278202
0.6508 Remote Similarity NPC222852
0.6508 Remote Similarity NPC475931
0.65 Remote Similarity NPC87564
0.65 Remote Similarity NPC154245
0.65 Remote Similarity NPC88966
0.65 Remote Similarity NPC424
0.65 Remote Similarity NPC25417
0.65 Remote Similarity NPC6095
0.65 Remote Similarity NPC261831
0.65 Remote Similarity NPC290563
0.65 Remote Similarity NPC281972
0.65 Remote Similarity NPC300121
0.65 Remote Similarity NPC32467
0.65 Remote Similarity NPC85813
0.6491 Remote Similarity NPC207815

  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 NPC26102 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
0.6875 Remote Similarity NPD3197 Phase 1
0.6667 Remote Similarity NPD4246 Clinical (unspecified phase)
0.6545 Remote Similarity NPD4265 Approved
0.65 Remote Similarity NPD3195 Phase 2
0.65 Remote Similarity NPD3194 Approved
0.65 Remote Similarity NPD3196 Approved
0.65 Remote Similarity NPD4266 Approved
0.6333 Remote Similarity NPD3172 Approved
0.6212 Remote Similarity NPD3210 Clinical (unspecified phase)
0.6 Remote Similarity NPD29 Approved
0.6 Remote Similarity NPD28 Approved
0.5965 Remote Similarity NPD39 Approved
0.5949 Remote Similarity NPD5331 Approved
0.5949 Remote Similarity NPD5332 Approved
0.5946 Remote Similarity NPD8264 Approved
0.5932 Remote Similarity NPD3173 Approved
0.5873 Remote Similarity NPD342 Phase 1
0.5857 Remote Similarity NPD4247 Clinical (unspecified phase)
0.5846 Remote Similarity NPD6109 Phase 1
0.5844 Remote Similarity NPD6683 Phase 2
0.5833 Remote Similarity NPD7143 Approved
0.5833 Remote Similarity NPD7144 Approved
0.5821 Remote Similarity NPD6949 Clinical (unspecified phase)
0.5821 Remote Similarity NPD368 Approved
0.5811 Remote Similarity NPD6924 Approved
0.5811 Remote Similarity NPD6926 Approved
0.58 Remote Similarity NPD2272 Approved
0.58 Remote Similarity NPD5383 Approved
0.5763 Remote Similarity NPD622 Approved
0.5753 Remote Similarity NPD7152 Approved
0.5753 Remote Similarity NPD7150 Approved
0.5753 Remote Similarity NPD7151 Approved
0.5714 Remote Similarity NPD4268 Approved
0.5714 Remote Similarity NPD4271 Approved
0.5696 Remote Similarity NPD6898 Phase 1
0.5694 Remote Similarity NPD6922 Approved
0.5694 Remote Similarity NPD6923 Approved
0.569 Remote Similarity NPD4222 Approved
0.5663 Remote Similarity NPD7750 Discontinued
0.5658 Remote Similarity NPD6933 Approved
0.5625 Remote Similarity NPD4627 Clinical (unspecified phase)
0.5616 Remote Similarity NPD3212 Clinical (unspecified phase)
0.5614 Remote Similarity NPD5326 Phase 3
0.561 Remote Similarity NPD6082 Clinical (unspecified phase)

  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