Structure

Physi-Chem Properties

Molecular Weight:  297.25
Volume:  340.634
LogP:  6.253
LogD:  5.304
LogS:  -6.136
# Rotatable Bonds:  0
TPSA:  23.79
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  4
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.535
Synthetic Accessibility Score:  5.082
Fsp3:  0.857
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.679
MDCK Permeability:  3.6291341530159116e-05
Pgp-inhibitor:  0.982
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.742
30% Bioavailability (F30%):  0.014

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.581
Plasma Protein Binding (PPB):  91.08247375488281%
Volume Distribution (VD):  1.805
Pgp-substrate:  9.87924575805664%

ADMET: Metabolism

CYP1A2-inhibitor:  0.553
CYP1A2-substrate:  0.682
CYP2C19-inhibitor:  0.551
CYP2C19-substrate:  0.841
CYP2C9-inhibitor:  0.49
CYP2C9-substrate:  0.204
CYP2D6-inhibitor:  0.051
CYP2D6-substrate:  0.079
CYP3A4-inhibitor:  0.94
CYP3A4-substrate:  0.443

ADMET: Excretion

Clearance (CL):  15.206
Half-life (T1/2):  0.138

ADMET: Toxicity

hERG Blockers:  0.037
Human Hepatotoxicity (H-HT):  0.349
Drug-inuced Liver Injury (DILI):  0.841
AMES Toxicity:  0.057
Rat Oral Acute Toxicity:  0.945
Maximum Recommended Daily Dose:  0.911
Skin Sensitization:  0.72
Carcinogencity:  0.732
Eye Corrosion:  0.941
Eye Irritation:  0.449
Respiratory Toxicity:  0.985

Download Data

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

  Natural Product: NPC474455

Natural Product ID:  NPC474455
Common Name*:   (1S,3Ar,4S,5As,10As,10Br,10Cs)-1,4,7,7-Tetramethyl-2,3,3A,4,5,5A,6,8,10,10A,10B,10C-Dodecahydropyrene-1-Carbonitrile
IUPAC Name:   (1S,3aR,4S,5aS,10aS,10bR,10cS)-1,4,7,7-tetramethyl-2,3,3a,4,5,5a,6,8,10,10a,10b,10c-dodecahydropyrene-1-carbonitrile
Synonyms:  
Standard InCHIKey:  YQIDYSXUAWORQB-CFYDALQJSA-N
Standard InCHI:  InChI=1S/C21H31N/c1-13-9-15-11-20(2,3)10-14-5-6-17-19(18(14)15)16(13)7-8-21(17,4)12-22/h5,13,15-19H,6-11H2,1-4H3/t13-,15-,16+,17-,18-,19+,21+/m0/s1
SMILES:  N#C[C@@]1(C)CC[C@H]2[C@@H]3[C@@H]1CC=C1[C@H]3[C@@H](C[C@@H]2C)CC(C1)(C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL469277
PubChem CID:   44566840
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]

*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
NPO30160 Cymbastela hooperi Species Axinellidae Eukaryota n.a. n.a. n.a. PMID[19199790]
NPO30160 Cymbastela hooperi Species Axinellidae Eukaryota n.a. n.a. n.a. PMID[19299148]
NPO30160 Cymbastela hooperi Species Axinellidae Eukaryota n.a. n.a. n.a. PMID[8759172]

☑ 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 > 20.0 ug.mL-1 PMID[543231]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 0.0849 ug.mL-1 PMID[543231]
NPT2 Others Unspecified Ratio IC50 > 240.0 n.a. PMID[543231]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 0.0284 ug.mL-1 PMID[543231]
NPT2 Others Unspecified Ratio IC50 > 700.0 n.a. PMID[543231]

☑ 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 NPC474455 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 NPC474420
1.0 High Similarity NPC474454
0.9636 High Similarity NPC475696
0.9636 High Similarity NPC474457
0.9636 High Similarity NPC474415
0.9636 High Similarity NPC474528
0.9298 High Similarity NPC475716
0.8909 High Similarity NPC474416
0.8364 Intermediate Similarity NPC476681
0.8276 Intermediate Similarity NPC469770
0.8226 Intermediate Similarity NPC474086
0.7931 Intermediate Similarity NPC476679
0.7857 Intermediate Similarity NPC17518
0.7857 Intermediate Similarity NPC22765
0.7636 Intermediate Similarity NPC86683
0.7619 Intermediate Similarity NPC317778
0.75 Intermediate Similarity NPC184919
0.75 Intermediate Similarity NPC138409
0.7368 Intermediate Similarity NPC124851
0.7313 Intermediate Similarity NPC474456
0.7273 Intermediate Similarity NPC192529
0.7188 Intermediate Similarity NPC472827
0.7143 Intermediate Similarity NPC202189
0.7097 Intermediate Similarity NPC123194
0.7091 Intermediate Similarity NPC193180
0.7077 Intermediate Similarity NPC311809
0.7051 Intermediate Similarity NPC477289
0.7049 Intermediate Similarity NPC127944
0.7031 Intermediate Similarity NPC469769
0.7018 Intermediate Similarity NPC13991
0.7018 Intermediate Similarity NPC296337
0.7018 Intermediate Similarity NPC241784
0.7018 Intermediate Similarity NPC114239
0.6984 Remote Similarity NPC318036
0.697 Remote Similarity NPC219621
0.6909 Remote Similarity NPC103290
0.6892 Remote Similarity NPC476308
0.6875 Remote Similarity NPC470369
0.6875 Remote Similarity NPC173815
0.6875 Remote Similarity NPC470370
0.6857 Remote Similarity NPC296697
0.6857 Remote Similarity NPC39157
0.6857 Remote Similarity NPC82477
0.6857 Remote Similarity NPC142754
0.6842 Remote Similarity NPC248411
0.6806 Remote Similarity NPC265789
0.6806 Remote Similarity NPC21773
0.6786 Remote Similarity NPC190232
0.6786 Remote Similarity NPC105246
0.6769 Remote Similarity NPC324944
0.6765 Remote Similarity NPC469662
0.6761 Remote Similarity NPC286814
0.6714 Remote Similarity NPC20181
0.6714 Remote Similarity NPC220210
0.6667 Remote Similarity NPC476683
0.6622 Remote Similarity NPC476904
0.6618 Remote Similarity NPC202118
0.6618 Remote Similarity NPC145715
0.6618 Remote Similarity NPC197238
0.6613 Remote Similarity NPC473728
0.6575 Remote Similarity NPC190035
0.6571 Remote Similarity NPC92327
0.6571 Remote Similarity NPC286669
0.6571 Remote Similarity NPC222366
0.6571 Remote Similarity NPC476039
0.6562 Remote Similarity NPC470893
0.6557 Remote Similarity NPC200129
0.6522 Remote Similarity NPC473959
0.6515 Remote Similarity NPC60772
0.6486 Remote Similarity NPC474488
0.6479 Remote Similarity NPC197805
0.6479 Remote Similarity NPC176107
0.6471 Remote Similarity NPC469728
0.6447 Remote Similarity NPC7214
0.6418 Remote Similarity NPC28755
0.6418 Remote Similarity NPC152211
0.64 Remote Similarity NPC100334
0.64 Remote Similarity NPC211641
0.6393 Remote Similarity NPC17810
0.6389 Remote Similarity NPC20610
0.6389 Remote Similarity NPC94192
0.6364 Remote Similarity NPC139717
0.6364 Remote Similarity NPC297643
0.6364 Remote Similarity NPC229262
0.6351 Remote Similarity NPC476329
0.6351 Remote Similarity NPC225467
0.6338 Remote Similarity NPC323005
0.6338 Remote Similarity NPC37792
0.6329 Remote Similarity NPC12035
0.6316 Remote Similarity NPC293803
0.6301 Remote Similarity NPC139397
0.6301 Remote Similarity NPC182815
0.625 Remote Similarity NPC193770
0.6234 Remote Similarity NPC112680
0.6234 Remote Similarity NPC106364
0.6234 Remote Similarity NPC120098
0.6234 Remote Similarity NPC290598
0.6234 Remote Similarity NPC27765
0.6234 Remote Similarity NPC122418
0.6234 Remote Similarity NPC265328
0.6234 Remote Similarity NPC30590
0.6216 Remote Similarity NPC2634
0.6216 Remote Similarity NPC214770
0.6216 Remote Similarity NPC475728
0.6216 Remote Similarity NPC477856
0.6216 Remote Similarity NPC260040
0.6216 Remote Similarity NPC282593
0.6216 Remote Similarity NPC265782
0.6216 Remote Similarity NPC307176
0.6216 Remote Similarity NPC159577
0.6216 Remote Similarity NPC251929
0.6216 Remote Similarity NPC35734
0.6207 Remote Similarity NPC177470
0.6203 Remote Similarity NPC211322
0.6197 Remote Similarity NPC163678
0.6184 Remote Similarity NPC219232
0.6184 Remote Similarity NPC128346
0.6182 Remote Similarity NPC190810
0.6182 Remote Similarity NPC76145
0.6182 Remote Similarity NPC34764
0.6167 Remote Similarity NPC49088
0.6164 Remote Similarity NPC260474
0.6164 Remote Similarity NPC188292
0.6164 Remote Similarity NPC216460
0.6164 Remote Similarity NPC32055
0.6164 Remote Similarity NPC310992
0.6154 Remote Similarity NPC472805
0.6154 Remote Similarity NPC101475
0.6154 Remote Similarity NPC471897
0.6154 Remote Similarity NPC40394
0.6154 Remote Similarity NPC107039
0.6154 Remote Similarity NPC34177
0.6154 Remote Similarity NPC90979
0.6154 Remote Similarity NPC157996
0.6154 Remote Similarity NPC471899
0.614 Remote Similarity NPC227632
0.614 Remote Similarity NPC78551
0.614 Remote Similarity NPC62086
0.6133 Remote Similarity NPC54123
0.6133 Remote Similarity NPC115023
0.6133 Remote Similarity NPC470078
0.6119 Remote Similarity NPC11130
0.6111 Remote Similarity NPC279434
0.6111 Remote Similarity NPC242945
0.6111 Remote Similarity NPC176171
0.6111 Remote Similarity NPC259156
0.6104 Remote Similarity NPC34700
0.6104 Remote Similarity NPC138374
0.6104 Remote Similarity NPC125828
0.6102 Remote Similarity NPC86538
0.6102 Remote Similarity NPC109813
0.6102 Remote Similarity NPC60556
0.6098 Remote Similarity NPC171639
0.6087 Remote Similarity NPC127582
0.6087 Remote Similarity NPC176621
0.6081 Remote Similarity NPC472831
0.6076 Remote Similarity NPC99168
0.6076 Remote Similarity NPC253807
0.6076 Remote Similarity NPC22955
0.6076 Remote Similarity NPC260385
0.6076 Remote Similarity NPC110094
0.6076 Remote Similarity NPC474989
0.6076 Remote Similarity NPC158662
0.6076 Remote Similarity NPC115515
0.6076 Remote Similarity NPC300499
0.6076 Remote Similarity NPC196753
0.6076 Remote Similarity NPC470396
0.6076 Remote Similarity NPC230295
0.6076 Remote Similarity NPC98386
0.6076 Remote Similarity NPC280654
0.6066 Remote Similarity NPC323445
0.6056 Remote Similarity NPC285371
0.6056 Remote Similarity NPC169275
0.6056 Remote Similarity NPC52449
0.6056 Remote Similarity NPC475124
0.6053 Remote Similarity NPC474228
0.6053 Remote Similarity NPC471799
0.6053 Remote Similarity NPC182717
0.6053 Remote Similarity NPC303613
0.6053 Remote Similarity NPC251705
0.6053 Remote Similarity NPC474743
0.6049 Remote Similarity NPC152039
0.6049 Remote Similarity NPC118329
0.6049 Remote Similarity NPC329782
0.6034 Remote Similarity NPC144023
0.6029 Remote Similarity NPC472830
0.6026 Remote Similarity NPC89294
0.6026 Remote Similarity NPC292589
0.6 Remote Similarity NPC231431
0.6 Remote Similarity NPC40574
0.6 Remote Similarity NPC199595
0.6 Remote Similarity NPC53744
0.6 Remote Similarity NPC60565
0.6 Remote Similarity NPC145498
0.6 Remote Similarity NPC291379
0.6 Remote Similarity NPC16394
0.5976 Remote Similarity NPC215474
0.5976 Remote Similarity NPC283277
0.5976 Remote Similarity NPC472312
0.5974 Remote Similarity NPC241854

  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 NPC474455 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
0.7105 Intermediate Similarity NPD8028 Phase 2
0.6901 Remote Similarity NPD6938 Clinical (unspecified phase)
0.6901 Remote Similarity NPD6939 Phase 2
0.6786 Remote Similarity NPD1799 Clinical (unspecified phase)
0.6393 Remote Similarity NPD8262 Approved
0.6389 Remote Similarity NPD3621 Clinical (unspecified phase)
0.6301 Remote Similarity NPD4137 Phase 3
0.6216 Remote Similarity NPD4691 Approved
0.6216 Remote Similarity NPD4747 Approved
0.6182 Remote Similarity NPD319 Phase 1
0.6133 Remote Similarity NPD4243 Approved
0.6 Remote Similarity NPD7645 Phase 2
0.6 Remote Similarity NPD7614 Phase 1
0.6 Remote Similarity NPD7732 Phase 3
0.5974 Remote Similarity NPD4785 Approved
0.5974 Remote Similarity NPD4058 Approved
0.5974 Remote Similarity NPD4784 Approved
0.5897 Remote Similarity NPD6942 Approved
0.5897 Remote Similarity NPD7339 Approved
0.5897 Remote Similarity NPD4190 Phase 3
0.5897 Remote Similarity NPD5275 Approved
0.5823 Remote Similarity NPD3701 Clinical (unspecified phase)
0.5795 Remote Similarity NPD4096 Approved
0.5769 Remote Similarity NPD4687 Approved
0.5769 Remote Similarity NPD5733 Approved
0.5714 Remote Similarity NPD5276 Approved
0.5714 Remote Similarity NPD3527 Clinical (unspecified phase)
0.5714 Remote Similarity NPD5365 Phase 2
0.5647 Remote Similarity NPD4544 Approved
0.561 Remote Similarity NPD4195 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