Structure

Physi-Chem Properties

Molecular Weight:  349.08
Volume:  325.69
LogP:  4.446
LogD:  4.538
LogS:  -5.06
# Rotatable Bonds:  2
TPSA:  32.59
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  2
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.547
Synthetic Accessibility Score:  5.132
Fsp3:  0.688
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  2
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.838
MDCK Permeability:  1.2841277566622011e-05
Pgp-inhibitor:  0.005
Pgp-substrate:  0.034
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.001
30% Bioavailability (F30%):  0.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.962
Plasma Protein Binding (PPB):  78.03174591064453%
Volume Distribution (VD):  0.809
Pgp-substrate:  20.93372917175293%

ADMET: Metabolism

CYP1A2-inhibitor:  0.483
CYP1A2-substrate:  0.801
CYP2C19-inhibitor:  0.578
CYP2C19-substrate:  0.881
CYP2C9-inhibitor:  0.68
CYP2C9-substrate:  0.889
CYP2D6-inhibitor:  0.077
CYP2D6-substrate:  0.881
CYP3A4-inhibitor:  0.886
CYP3A4-substrate:  0.653

ADMET: Excretion

Clearance (CL):  2.031
Half-life (T1/2):  0.298

ADMET: Toxicity

hERG Blockers:  0.047
Human Hepatotoxicity (H-HT):  0.672
Drug-inuced Liver Injury (DILI):  0.065
AMES Toxicity:  0.05
Rat Oral Acute Toxicity:  0.461
Maximum Recommended Daily Dose:  0.931
Skin Sensitization:  0.686
Carcinogencity:  0.337
Eye Corrosion:  0.94
Eye Irritation:  0.24
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: NPC218902

Natural Product ID:  NPC218902
Common Name*:   Reticulidin B
IUPAC Name:   (2S,3R,4aR,8aS)-3-chloro-7-[(E)-2-(dichloromethylideneamino)ethenyl]-4,4,8a-trimethyl-1,2,3,4a,5,8-hexahydronaphthalen-2-ol
Synonyms:  
Standard InCHIKey:  JOJUODIBULSKBG-NNYSSPGYSA-N
Standard InCHI:  InChI=1S/C16H22Cl3NO/c1-15(2)12-5-4-10(6-7-20-14(18)19)8-16(12,3)9-11(21)13(15)17/h4,6-7,11-13,21H,5,8-9H2,1-3H3/b7-6+/t11-,12-,13-,16-/m0/s1
SMILES:  O[C@H]1C[C@]2(C)CC(=CC[C@H]2C([C@H]1Cl)(C)C)/C=C/N=C(Cl)Cl
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL447763
PubChem CID:   10736620
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004707] Organic nitrogen compounds
      • [CHEMONTID:0000278] Organonitrogen compounds
        • [CHEMONTID:0003272] Isocyanide dichlorides

*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
NPO13092 Reticulidia fungia Species Phyllidiidae Eukaryota n.a. n.a. n.a. PMID[10514331]
NPO13092 Reticulidia fungia Species Phyllidiidae 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
NPT91 Cell Line KB Homo sapiens IC50 = 0.42 ug.mL-1 PMID[487495]
NPT137 Cell Line L1210 Mus musculus IC50 = 0.11 ug.mL-1 PMID[487495]

☑ 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 NPC218902 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 NPC125771
0.7172 Intermediate Similarity NPC76164
0.7172 Intermediate Similarity NPC153699
0.6852 Remote Similarity NPC269713
0.6702 Remote Similarity NPC68443
0.6702 Remote Similarity NPC182717
0.6667 Remote Similarity NPC106432
0.663 Remote Similarity NPC208999
0.6596 Remote Similarity NPC110799
0.6531 Remote Similarity NPC307965
0.6531 Remote Similarity NPC76931
0.6531 Remote Similarity NPC18603
0.6531 Remote Similarity NPC205455
0.6531 Remote Similarity NPC318136
0.6531 Remote Similarity NPC186191
0.6526 Remote Similarity NPC471799
0.6495 Remote Similarity NPC470362
0.6495 Remote Similarity NPC134330
0.6495 Remote Similarity NPC129165
0.6495 Remote Similarity NPC265588
0.6489 Remote Similarity NPC145498
0.6489 Remote Similarity NPC92801
0.6484 Remote Similarity NPC475812
0.6458 Remote Similarity NPC243342
0.6458 Remote Similarity NPC91858
0.6458 Remote Similarity NPC100334
0.6458 Remote Similarity NPC471797
0.6458 Remote Similarity NPC477138
0.6452 Remote Similarity NPC32055
0.6452 Remote Similarity NPC216460
0.6452 Remote Similarity NPC96484
0.6429 Remote Similarity NPC471798
0.6421 Remote Similarity NPC164022
0.6421 Remote Similarity NPC242001
0.6421 Remote Similarity NPC167706
0.6417 Remote Similarity NPC216335
0.6413 Remote Similarity NPC149680
0.6392 Remote Similarity NPC291503
0.6392 Remote Similarity NPC257347
0.6392 Remote Similarity NPC471723
0.6392 Remote Similarity NPC141071
0.6389 Remote Similarity NPC280710
0.6389 Remote Similarity NPC243985
0.6383 Remote Similarity NPC476431
0.6373 Remote Similarity NPC237795
0.6373 Remote Similarity NPC82538
0.6364 Remote Similarity NPC72507
0.6356 Remote Similarity NPC7797
0.6344 Remote Similarity NPC197805
0.6327 Remote Similarity NPC265328
0.6327 Remote Similarity NPC253190
0.6327 Remote Similarity NPC122418
0.6327 Remote Similarity NPC202642
0.6327 Remote Similarity NPC189883
0.6327 Remote Similarity NPC30590
0.6327 Remote Similarity NPC27765
0.6327 Remote Similarity NPC113733
0.6327 Remote Similarity NPC120098
0.6327 Remote Similarity NPC290598
0.6327 Remote Similarity NPC46160
0.6316 Remote Similarity NPC34834
0.6311 Remote Similarity NPC231310
0.6311 Remote Similarity NPC238485
0.63 Remote Similarity NPC31330
0.6275 Remote Similarity NPC202389
0.6275 Remote Similarity NPC201852
0.6263 Remote Similarity NPC157996
0.6263 Remote Similarity NPC90979
0.6263 Remote Similarity NPC40394
0.6263 Remote Similarity NPC214570
0.6263 Remote Similarity NPC34177
0.6263 Remote Similarity NPC472805
0.6263 Remote Similarity NPC91594
0.6263 Remote Similarity NPC101475
0.625 Remote Similarity NPC109528
0.6237 Remote Similarity NPC286669
0.6237 Remote Similarity NPC222366
0.6237 Remote Similarity NPC476039
0.6226 Remote Similarity NPC34754
0.6224 Remote Similarity NPC288035
0.6224 Remote Similarity NPC69383
0.6224 Remote Similarity NPC22105
0.6224 Remote Similarity NPC230301
0.6224 Remote Similarity NPC471468
0.6224 Remote Similarity NPC134847
0.6224 Remote Similarity NPC66566
0.6224 Remote Similarity NPC477923
0.6224 Remote Similarity NPC121744
0.6224 Remote Similarity NPC28657
0.6224 Remote Similarity NPC304309
0.6224 Remote Similarity NPC162742
0.6224 Remote Similarity NPC34700
0.6224 Remote Similarity NPC138374
0.6224 Remote Similarity NPC313179
0.6224 Remote Similarity NPC118508
0.6224 Remote Similarity NPC322353
0.6224 Remote Similarity NPC136188
0.6224 Remote Similarity NPC171148
0.6224 Remote Similarity NPC285893
0.6216 Remote Similarity NPC240650
0.6214 Remote Similarity NPC474789
0.6214 Remote Similarity NPC52108
0.6214 Remote Similarity NPC470384
0.6211 Remote Similarity NPC474248
0.6211 Remote Similarity NPC471560
0.62 Remote Similarity NPC196753
0.62 Remote Similarity NPC83351
0.62 Remote Similarity NPC98386
0.62 Remote Similarity NPC230295
0.62 Remote Similarity NPC300499
0.62 Remote Similarity NPC253807
0.62 Remote Similarity NPC275910
0.62 Remote Similarity NPC474989
0.62 Remote Similarity NPC167891
0.62 Remote Similarity NPC22955
0.62 Remote Similarity NPC99168
0.62 Remote Similarity NPC470396
0.62 Remote Similarity NPC158662
0.6196 Remote Similarity NPC290367
0.6196 Remote Similarity NPC225415
0.6186 Remote Similarity NPC130665
0.6186 Remote Similarity NPC474140
0.6182 Remote Similarity NPC311164
0.6182 Remote Similarity NPC272732
0.6176 Remote Similarity NPC476646
0.6176 Remote Similarity NPC6707
0.6162 Remote Similarity NPC73875
0.6162 Remote Similarity NPC300324
0.6162 Remote Similarity NPC106364
0.6162 Remote Similarity NPC274079
0.6162 Remote Similarity NPC237460
0.6162 Remote Similarity NPC107059
0.6162 Remote Similarity NPC321381
0.6162 Remote Similarity NPC477925
0.6162 Remote Similarity NPC321016
0.6162 Remote Similarity NPC96319
0.6162 Remote Similarity NPC240604
0.6154 Remote Similarity NPC474493
0.6139 Remote Similarity NPC53744
0.6139 Remote Similarity NPC30986
0.6139 Remote Similarity NPC209430
0.6139 Remote Similarity NPC291379
0.6139 Remote Similarity NPC1319
0.6129 Remote Similarity NPC163678
0.6126 Remote Similarity NPC476903
0.6122 Remote Similarity NPC469533
0.6122 Remote Similarity NPC469593
0.6122 Remote Similarity NPC201048
0.6122 Remote Similarity NPC476366
0.6122 Remote Similarity NPC469534
0.6122 Remote Similarity NPC306727
0.6117 Remote Similarity NPC87489
0.6117 Remote Similarity NPC20853
0.6105 Remote Similarity NPC471238
0.61 Remote Similarity NPC34019
0.61 Remote Similarity NPC130136
0.61 Remote Similarity NPC477924
0.61 Remote Similarity NPC470758
0.61 Remote Similarity NPC470711
0.61 Remote Similarity NPC155986
0.61 Remote Similarity NPC318495
0.61 Remote Similarity NPC198968
0.6091 Remote Similarity NPC473314
0.6087 Remote Similarity NPC45365
0.6087 Remote Similarity NPC293299
0.6082 Remote Similarity NPC242992
0.6082 Remote Similarity NPC23954
0.6078 Remote Similarity NPC209944
0.6078 Remote Similarity NPC241290
0.6078 Remote Similarity NPC295131
0.6078 Remote Similarity NPC96362
0.6078 Remote Similarity NPC164840
0.6078 Remote Similarity NPC236112
0.6078 Remote Similarity NPC287749
0.6078 Remote Similarity NPC234193
0.6071 Remote Similarity NPC140300
0.6068 Remote Similarity NPC169375
0.6064 Remote Similarity NPC202017
0.6064 Remote Similarity NPC279434
0.6058 Remote Similarity NPC97491
0.6058 Remote Similarity NPC57370
0.6058 Remote Similarity NPC273356
0.6058 Remote Similarity NPC312480
0.6042 Remote Similarity NPC9942
0.604 Remote Similarity NPC138621
0.604 Remote Similarity NPC65897
0.604 Remote Similarity NPC302041
0.604 Remote Similarity NPC473943
0.604 Remote Similarity NPC167037
0.604 Remote Similarity NPC285761
0.604 Remote Similarity NPC6978
0.604 Remote Similarity NPC87604
0.604 Remote Similarity NPC11908
0.604 Remote Similarity NPC312328
0.604 Remote Similarity NPC244385
0.604 Remote Similarity NPC474216
0.604 Remote Similarity NPC477522
0.604 Remote Similarity NPC476314
0.604 Remote Similarity NPC85346
0.604 Remote Similarity NPC274750

  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 NPC218902 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
0.6387 Remote Similarity NPD5167 Approved
0.6293 Remote Similarity NPD5168 Approved
0.6224 Remote Similarity NPD6942 Approved
0.6224 Remote Similarity NPD7339 Approved
0.6224 Remote Similarity NPD8264 Approved
0.6162 Remote Similarity NPD3701 Clinical (unspecified phase)
0.6139 Remote Similarity NPD7645 Phase 2
0.6134 Remote Similarity NPD5215 Approved
0.6134 Remote Similarity NPD5217 Approved
0.6134 Remote Similarity NPD5216 Approved
0.6082 Remote Similarity NPD7150 Approved
0.6082 Remote Similarity NPD7152 Approved
0.6082 Remote Similarity NPD7151 Approved
0.5979 Remote Similarity NPD7143 Approved
0.5979 Remote Similarity NPD7144 Approved
0.596 Remote Similarity NPD6926 Approved
0.596 Remote Similarity NPD6924 Approved
0.5935 Remote Similarity NPD6868 Approved
0.5922 Remote Similarity NPD7525 Registered
0.5876 Remote Similarity NPD6922 Approved
0.5876 Remote Similarity NPD6923 Approved
0.5842 Remote Similarity NPD6933 Approved
0.581 Remote Similarity NPD3667 Approved
0.5794 Remote Similarity NPD7100 Approved
0.5794 Remote Similarity NPD7101 Approved
0.5785 Remote Similarity NPD5169 Approved
0.5769 Remote Similarity NPD7509 Discontinued
0.5741 Remote Similarity NPD3618 Phase 1
0.5738 Remote Similarity NPD5127 Approved
0.5701 Remote Similarity NPD4786 Approved
0.5673 Remote Similarity NPD6929 Approved
0.5669 Remote Similarity NPD4522 Approved
0.5644 Remote Similarity NPD4784 Approved
0.5644 Remote Similarity NPD4785 Approved
0.5631 Remote Similarity NPD6932 Approved
0.5625 Remote Similarity NPD6079 Approved
0.5619 Remote Similarity NPD4748 Discontinued
0.5619 Remote Similarity NPD6930 Phase 2
0.5619 Remote Similarity NPD6931 Approved
0.56 Remote Similarity NPD4243 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