Structure

Physi-Chem Properties

Molecular Weight:  283.19
Volume:  318.115
LogP:  4.601
LogD:  3.803
LogS:  -5.654
# Rotatable Bonds:  0
TPSA:  29.43
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  3
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.478
Synthetic Accessibility Score:  4.773
Fsp3:  0.579
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.804
MDCK Permeability:  1.98E-05
Pgp-inhibitor:  0.829
Pgp-substrate:  0.25
Human Intestinal Absorption (HIA):  0.024
20% Bioavailability (F20%):  0.756
30% Bioavailability (F30%):  0.138

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.323
Plasma Protein Binding (PPB):  93.29%
Volume Distribution (VD):  2.321
Pgp-substrate:  4.51%

ADMET: Metabolism

CYP1A2-inhibitor:  0.173
CYP1A2-substrate:  0.383
CYP2C19-inhibitor:  0.613
CYP2C19-substrate:  0.905
CYP2C9-inhibitor:  0.241
CYP2C9-substrate:  0.07
CYP2D6-inhibitor:  0.322
CYP2D6-substrate:  0.098
CYP3A4-inhibitor:  0.776
CYP3A4-substrate:  0.702

ADMET: Excretion

Clearance (CL):  3.779
Half-life (T1/2):  0.123

ADMET: Toxicity

hERG Blockers:  0.011
Human Hepatotoxicity (H-HT):  0.669
Drug-inuced Liver Injury (DILI):  0.23
AMES Toxicity:  0.006
Rat Oral Acute Toxicity:  0.362
Maximum Recommended Daily Dose:  0.924
Skin Sensitization:  0.27
Carcinogencity:  0.916
Eye Corrosion:  0.004
Eye Irritation:  0.013
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: NPC477582

Natural Product ID:  NPC477582
Common Name*:   Nigelladine B
IUPAC Name:   (8aS)-2,2,4,8a-tetramethyl-6-propan-2-yl-8,9-dihydrocyclopenta[g]quinolin-7-one
Synonyms:  
Standard InCHIKey:  ZNCHZFFUPFZQEP-IBGZPJMESA-N
Standard InCHI:  InChI=1S/C19H25NO/c1-11(2)17-14-7-13-12(3)8-18(4,5)20-15(13)9-19(14,6)10-16(17)21/h7-8,11H,9-10H2,1-6H3/t19-/m0/s1
SMILES:  CC1=CC(N=C2C1=CC3=C(C(=O)C[C@@]3(C2)C)C(C)C)(C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   86302611
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids

*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
NPO2136 Nigella glandulifera Species Ranunculaceae Eukaryota Seeds n.a. n.a. PMID[24593120]
NPO2136 Nigella glandulifera Species Ranunculaceae Eukaryota n.a. n.a. n.a. PMID[26227777]
NPO2136 Nigella glandulifera Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2136 Nigella glandulifera Species Ranunculaceae 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
NPT178 Individual Protein Protein-tyrosine phosphatase 1B Homo sapiens IC50 = 9710 nM PMID[24593120]

☑ 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 NPC477582 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
0.9868 High Similarity NPC477581
0.9868 High Similarity NPC477583
0.8537 High Similarity NPC477584
0.7753 Intermediate Similarity NPC249312
0.6941 Remote Similarity NPC473171
0.6835 Remote Similarity NPC165695
0.6829 Remote Similarity NPC310992
0.6786 Remote Similarity NPC181204
0.6753 Remote Similarity NPC266295
0.6753 Remote Similarity NPC27610
0.6753 Remote Similarity NPC56905
0.6753 Remote Similarity NPC94991
0.6747 Remote Similarity NPC139397
0.6747 Remote Similarity NPC256846
0.6742 Remote Similarity NPC250632
0.6735 Remote Similarity NPC247220
0.6709 Remote Similarity NPC97322
0.6667 Remote Similarity NPC259261
0.6667 Remote Similarity NPC251929
0.6667 Remote Similarity NPC35734
0.6667 Remote Similarity NPC282593
0.6667 Remote Similarity NPC2634
0.6667 Remote Similarity NPC260040
0.6667 Remote Similarity NPC307176
0.6667 Remote Similarity NPC251118
0.6667 Remote Similarity NPC265782
0.6667 Remote Similarity NPC159577
0.6628 Remote Similarity NPC474796
0.6628 Remote Similarity NPC329866
0.6628 Remote Similarity NPC474797
0.6625 Remote Similarity NPC167256
0.66 Remote Similarity NPC140685
0.6588 Remote Similarity NPC470078
0.6588 Remote Similarity NPC54123
0.6588 Remote Similarity NPC115023
0.6582 Remote Similarity NPC25853
0.6582 Remote Similarity NPC127582
0.6569 Remote Similarity NPC226509
0.6543 Remote Similarity NPC475124
0.6543 Remote Similarity NPC285371
0.6543 Remote Similarity NPC212210
0.6543 Remote Similarity NPC4638
0.6512 Remote Similarity NPC470045
0.6512 Remote Similarity NPC251705
0.6512 Remote Similarity NPC474228
0.6512 Remote Similarity NPC303613
0.6512 Remote Similarity NPC470044
0.65 Remote Similarity NPC213152
0.6477 Remote Similarity NPC469793
0.6477 Remote Similarity NPC469796
0.6456 Remote Similarity NPC472304
0.6456 Remote Similarity NPC276764
0.6444 Remote Similarity NPC170793
0.6429 Remote Similarity NPC20610
0.6429 Remote Similarity NPC260474
0.6429 Remote Similarity NPC87141
0.6429 Remote Similarity NPC188292
0.642 Remote Similarity NPC32285
0.641 Remote Similarity NPC115385
0.641 Remote Similarity NPC230823
0.641 Remote Similarity NPC267626
0.641 Remote Similarity NPC49575
0.641 Remote Similarity NPC55004
0.6408 Remote Similarity NPC152718
0.6395 Remote Similarity NPC234707
0.6395 Remote Similarity NPC5701
0.6386 Remote Similarity NPC323005
0.6383 Remote Similarity NPC76283
0.6364 Remote Similarity NPC293803
0.6353 Remote Similarity NPC182815
0.6341 Remote Similarity NPC469662
0.6341 Remote Similarity NPC6697
0.6341 Remote Similarity NPC473902
0.6329 Remote Similarity NPC30215
0.6316 Remote Similarity NPC45283
0.6316 Remote Similarity NPC474141
0.6316 Remote Similarity NPC268564
0.631 Remote Similarity NPC475523
0.6292 Remote Similarity NPC69408
0.6286 Remote Similarity NPC469958
0.6282 Remote Similarity NPC20603
0.6279 Remote Similarity NPC246722
0.6279 Remote Similarity NPC151045
0.625 Remote Similarity NPC255021
0.625 Remote Similarity NPC143834
0.625 Remote Similarity NPC309852
0.6235 Remote Similarity NPC155198
0.6226 Remote Similarity NPC230677
0.6222 Remote Similarity NPC283087
0.622 Remote Similarity NPC197238
0.622 Remote Similarity NPC288253
0.622 Remote Similarity NPC202118
0.622 Remote Similarity NPC472306
0.6211 Remote Similarity NPC311769
0.6211 Remote Similarity NPC182106
0.6207 Remote Similarity NPC305501
0.6207 Remote Similarity NPC190035
0.619 Remote Similarity NPC187315
0.617 Remote Similarity NPC21667
0.6154 Remote Similarity NPC189485
0.6147 Remote Similarity NPC476290
0.6146 Remote Similarity NPC476141
0.6145 Remote Similarity NPC150162
0.6136 Remote Similarity NPC130016
0.6136 Remote Similarity NPC109576
0.6136 Remote Similarity NPC180015
0.6136 Remote Similarity NPC56747
0.6133 Remote Similarity NPC32351
0.6125 Remote Similarity NPC308108
0.6125 Remote Similarity NPC170799
0.6118 Remote Similarity NPC193770
0.6111 Remote Similarity NPC110725
0.6105 Remote Similarity NPC87552
0.6104 Remote Similarity NPC37644
0.6104 Remote Similarity NPC296311
0.6098 Remote Similarity NPC475795
0.6098 Remote Similarity NPC60565
0.6095 Remote Similarity NPC469598
0.6095 Remote Similarity NPC58200
0.6092 Remote Similarity NPC214770
0.6092 Remote Similarity NPC477856
0.6087 Remote Similarity NPC27817
0.6087 Remote Similarity NPC471597
0.6087 Remote Similarity NPC90965
0.6078 Remote Similarity NPC476449
0.6076 Remote Similarity NPC473733
0.6071 Remote Similarity NPC470329
0.6064 Remote Similarity NPC469806
0.6064 Remote Similarity NPC472867
0.6064 Remote Similarity NPC268122
0.6064 Remote Similarity NPC469799
0.6064 Remote Similarity NPC469805
0.6064 Remote Similarity NPC469804
0.6055 Remote Similarity NPC175585
0.6053 Remote Similarity NPC64866
0.6049 Remote Similarity NPC285594
0.6049 Remote Similarity NPC96551
0.6047 Remote Similarity NPC82477
0.6047 Remote Similarity NPC296697
0.6047 Remote Similarity NPC39157
0.6047 Remote Similarity NPC142754
0.604 Remote Similarity NPC476754
0.604 Remote Similarity NPC477290
0.6036 Remote Similarity NPC476269
0.6023 Remote Similarity NPC474562
0.6023 Remote Similarity NPC225467
0.6023 Remote Similarity NPC223187
0.6022 Remote Similarity NPC469797
0.6022 Remote Similarity NPC474509
0.6022 Remote Similarity NPC469798
0.602 Remote Similarity NPC259252
0.6 Remote Similarity NPC118423
0.6 Remote Similarity NPC176171
0.6 Remote Similarity NPC255650
0.6 Remote Similarity NPC3856
0.6 Remote Similarity NPC279639
0.6 Remote Similarity NPC65650
0.6 Remote Similarity NPC474790
0.6 Remote Similarity NPC474976
0.6 Remote Similarity NPC92327
0.6 Remote Similarity NPC314500
0.6 Remote Similarity NPC476346
0.5978 Remote Similarity NPC469996
0.5977 Remote Similarity NPC286814
0.5977 Remote Similarity NPC474060
0.5957 Remote Similarity NPC477372
0.5957 Remote Similarity NPC4166
0.5957 Remote Similarity NPC121984
0.5949 Remote Similarity NPC275472
0.5941 Remote Similarity NPC247316
0.5934 Remote Similarity NPC40353
0.5934 Remote Similarity NPC1254
0.5934 Remote Similarity NPC180886
0.593 Remote Similarity NPC4370
0.593 Remote Similarity NPC290350
0.593 Remote Similarity NPC20181
0.593 Remote Similarity NPC176107
0.593 Remote Similarity NPC220210
0.5926 Remote Similarity NPC311852
0.5921 Remote Similarity NPC116906
0.5921 Remote Similarity NPC176819
0.5921 Remote Similarity NPC163984
0.5921 Remote Similarity NPC58970
0.5918 Remote Similarity NPC472614
0.5918 Remote Similarity NPC75315
0.5918 Remote Similarity NPC136548
0.5918 Remote Similarity NPC163016
0.5909 Remote Similarity NPC40574
0.59 Remote Similarity NPC477288
0.59 Remote Similarity NPC474964
0.5897 Remote Similarity NPC295777
0.5897 Remote Similarity NPC69898
0.5895 Remote Similarity NPC142253
0.5895 Remote Similarity NPC320514
0.5895 Remote Similarity NPC472239
0.5895 Remote Similarity NPC3511
0.5895 Remote Similarity NPC193347
0.5895 Remote Similarity NPC311092
0.5888 Remote Similarity NPC474563
0.5882 Remote Similarity NPC268039

  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 NPC477582 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
0.6889 Remote Similarity NPD3527 Clinical (unspecified phase)
0.6824 Remote Similarity NPD4058 Approved
0.6824 Remote Similarity NPD4687 Approved
0.6824 Remote Similarity NPD5733 Approved
0.6786 Remote Similarity NPD5276 Approved
0.6747 Remote Similarity NPD4137 Phase 3
0.67 Remote Similarity NPD6404 Discontinued
0.6667 Remote Similarity NPD4747 Approved
0.6667 Remote Similarity NPD4691 Approved
0.6429 Remote Similarity NPD3621 Clinical (unspecified phase)
0.6364 Remote Similarity NPD5769 Clinical (unspecified phase)
0.6125 Remote Similarity NPD287 Approved
0.6092 Remote Similarity NPD6938 Clinical (unspecified phase)
0.6092 Remote Similarity NPD6939 Phase 2
0.6061 Remote Similarity NPD4096 Approved
0.5979 Remote Similarity NPD4694 Approved
0.5979 Remote Similarity NPD5280 Approved
0.5957 Remote Similarity NPD8028 Phase 2
0.5895 Remote Similarity NPD4221 Approved
0.5895 Remote Similarity NPD4223 Phase 3
0.5833 Remote Similarity NPD7812 Clinical (unspecified phase)
0.5816 Remote Similarity NPD5279 Phase 3
0.5795 Remote Similarity NPD791 Approved
0.5795 Remote Similarity NPD15 Approved
0.5773 Remote Similarity NPD4197 Approved
0.5773 Remote Similarity NPD3133 Approved
0.5773 Remote Similarity NPD3666 Approved
0.5773 Remote Similarity NPD3665 Phase 1
0.5761 Remote Similarity NPD1346 Approved
0.5743 Remote Similarity NPD5692 Phase 3
0.5743 Remote Similarity NPD5207 Approved
0.5714 Remote Similarity NPD5329 Approved
0.57 Remote Similarity NPD4518 Approved
0.5686 Remote Similarity NPD6050 Approved
0.5686 Remote Similarity NPD5694 Approved
0.5686 Remote Similarity NPD5281 Approved
0.5686 Remote Similarity NPD5284 Approved
0.5657 Remote Similarity NPD6409 Approved
0.5657 Remote Similarity NPD3618 Phase 1
0.5657 Remote Similarity NPD4519 Discontinued
0.5657 Remote Similarity NPD7146 Approved
0.5657 Remote Similarity NPD4689 Approved
0.5657 Remote Similarity NPD4688 Approved
0.5657 Remote Similarity NPD5330 Approved
0.5657 Remote Similarity NPD4693 Phase 3
0.5657 Remote Similarity NPD7521 Approved
0.5657 Remote Similarity NPD5205 Approved
0.5657 Remote Similarity NPD7334 Approved
0.5657 Remote Similarity NPD4138 Approved
0.5657 Remote Similarity NPD4690 Approved
0.5657 Remote Similarity NPD4623 Approved
0.5657 Remote Similarity NPD5690 Phase 2
0.5657 Remote Similarity NPD6684 Approved
0.5638 Remote Similarity NPD3617 Approved
0.5638 Remote Similarity NPD1402 Approved
0.5632 Remote Similarity NPD7331 Phase 2
0.561 Remote Similarity NPD6330 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