NPASS Compound

Structure

NPC24617 OpenBabel07101719402D 73 74 0 0 1 0 0 0 0 0999 V2000 4.8531 -8.9701 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.4512 -7.4701 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2309 -7.4662 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9333 -2.0419 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0103 -5.7145 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4308 -6.8229 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7191 -10.4701 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.0493 -7.9701 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.1832 -7.4701 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.0493 -8.9701 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8128 -1.8787 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3577 0.6872 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.3172 -7.9701 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.1832 -9.4701 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5237 -2.8360 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3632 0.5826 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9871 -7.4701 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9871 -6.4701 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1633 -7.8776 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1076 -7.5487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1282 -1.1498 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7644 1.6007 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7191 -7.4701 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.4512 -9.4701 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8739 -0.6525 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8531 -7.9701 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5852 -7.9701 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5165 -6.7666 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.0115 -2.4294 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.0730 -5.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.3172 -8.9701 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1211 -5.9701 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.5501 -3.0644 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.9564 -0.3309 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.1668 -7.9612 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.9781 -0.2079 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 6.5852 -8.9701 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.6309 -1.3060 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9406 -6.9953 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7328 -7.3877 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5115 -1.5634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3013 -4.3924 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6547 -4.0589 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9991 -0.0419 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1249 -8.9604 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3070 0.7365 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3908 0.0359 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1657 2.6188 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0754 -0.6931 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 5.6798 0.9932 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -6.1602 2.7233 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -4.5779 3.4278 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 4.4172 -0.1924 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -4.7590 1.7052 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -4.2804 -3.3926 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 3.2016 -2.1271 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 3.5086 -5.0482 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -2.8118 -0.8489 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.8192 -7.7945 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -3.6097 -6.2522 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 3.3740 -0.6368 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.5940 -7.7523 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.2508 -8.2431 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3080 -0.9588 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.2959 -4.4969 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.6544 -4.0799 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.1659 0.9441 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9692 -9.4962 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.7613 -9.4237 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.2893 0.9238 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.6536 1.4935 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.7191 -9.4701 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 26 1 0 0 0 0 5 30 2 0 0 0 0 6 61 1 0 0 0 0 7 73 1 0 0 0 0 8 9 2 0 0 0 0 8 10 1 0 0 0 0 9 13 1 0 0 0 0 10 14 2 0 0 0 0 11 15 1 0 0 0 0 11 21 1 0 0 0 0 12 16 1 0 0 0 0 12 22 1 0 0 0 0 13 31 2 0 0 0 0 14 31 1 0 0 0 0 17 18 2 0 0 0 0 17 26 1 0 0 0 0 19 20 1 0 0 0 0 19 35 1 0 0 0 0 20 39 1 0 0 0 0 21 53 1 0 0 0 0 22 54 1 0 0 0 0 23 26 2 0 0 0 0 23 27 1 0 0 0 0 24 31 1 0 0 0 0 25 36 1 0 0 0 0 25 38 1 0 0 0 0 27 2 1 6 0 0 0 27 37 1 0 0 0 0 28 3 1 6 0 0 0 28 32 1 0 0 0 0 28 40 1 0 0 0 0 29 4 1 6 0 0 0 29 41 1 0 0 0 0 29 55 1 0 0 0 0 30 42 1 0 0 0 0 30 61 1 0 0 0 0 32 18 1 1 0 0 0 32 57 1 0 0 0 0 33 15 1 1 0 0 0 33 43 1 0 0 0 0 33 56 1 0 0 0 0 34 16 1 1 0 0 0 34 44 1 0 0 0 0 34 58 1 0 0 0 0 35 45 1 1 0 0 0 35 59 1 0 0 0 0 36 46 1 1 0 0 0 36 60 1 0 0 0 0 37 24 1 6 0 0 0 37 73 1 0 0 0 0 38 56 2 3 0 0 0 38 62 1 0 0 0 0 39 61 1 0 0 0 0 39 63 2 0 0 0 0 40 59 2 3 0 0 0 40 64 1 0 0 0 0 41 58 2 3 0 0 0 41 65 1 0 0 0 0 42 55 2 3 0 0 0 42 66 1 0 0 0 0 43 57 2 3 0 0 0 43 67 1 0 0 0 0 44 60 2 3 0 0 0 44 68 1 0 0 0 0 45 69 2 0 0 0 0 45 70 1 0 0 0 0 46 71 2 0 0 0 0 46 72 1 0 0 0 0 47 49 2 0 0 0 0 47 50 1 0 0 0 0 47 53 1 0 0 0 0 48 51 2 0 0 0 0 48 52 1 0 0 0 0 48 54 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	1023.55
Volume:	1025.272
LogP:	-2.428
LogD:	-0.173
LogS:	-2.845
# Rotatable Bonds:	19
TPSA:	409.52
# H-Bond Aceptor:	25
# H-Bond Donor:	16
# Rings:	2
# Heavy Atoms:	25

MedChem Properties

QED Drug-Likeness Score:	0.033
Synthetic Accessibility Score:	6.672
Fsp3:	0.521
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
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:	-7.161
MDCK Permeability:	2.0896593923680484e-05
Pgp-inhibitor:	0.001
Pgp-substrate:	1.0
Human Intestinal Absorption (HIA):	0.901
20% Bioavailability (F20%):	0.991
30% Bioavailability (F30%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.327
Plasma Protein Binding (PPB):	24.131656646728516%
Volume Distribution (VD):	0.538
Pgp-substrate:	62.56782913208008%

ADMET: Metabolism

CYP1A2-inhibitor:	0.0
CYP1A2-substrate:	0.001
CYP2C19-inhibitor:	0.013
CYP2C19-substrate:	0.02
CYP2C9-inhibitor:	0.087
CYP2C9-substrate:	0.062
CYP2D6-inhibitor:	0.001
CYP2D6-substrate:	0.085
CYP3A4-inhibitor:	0.006
CYP3A4-substrate:	0.0

ADMET: Excretion

Clearance (CL):	1.692
Half-life (T1/2):	0.771

ADMET: Toxicity

hERG Blockers:	0.031
Human Hepatotoxicity (H-HT):	0.992
Drug-inuced Liver Injury (DILI):	0.742
AMES Toxicity:	0.032
Rat Oral Acute Toxicity:	0.089
Maximum Recommended Daily Dose:	0.177
Skin Sensitization:	0.524
Carcinogencity:	0.041
Eye Corrosion:	0.003
Eye Irritation:	0.004
Respiratory Toxicity:	0.89

Download Data

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

Natural Product: NPC24617

Natural Product ID:	NPC24617
*Common Name:**	(5R,8S,11R,15S,18S,19S,22R)-8,15-Bis(3-Guanidinopropyl)-18-((1E,3E,5S,6S)-6-Methoxy-3,5-Dimethyl-7-Phenylhepta-1,3-Dienyl)-1,5,19-Trimethyl-2-Methylene-3,6,9,13,16,20,25-Heptaoxo-1,4,7,10,14,17,21-Heptaazacyclopentacosane-11,22-Dicarboxylic Acid
IUPAC Name:	(5R,8S,11R,15S,18S,19S,22R)-8,15-bis[3-(diaminomethylideneamino)propyl]-18-[(1E,3E,5S,6S)-6-methoxy-3,5-dimethyl-7-phenylhepta-1,3-dienyl]-1,5,19-trimethyl-2-methylidene-3,6,9,13,16,20,25-heptaoxo-1,4,7,10,14,17,21-heptazacyclopentacosane-11,22-dicarboxylic acid
Synonyms:
Standard InCHIKey:	UNKUVURYGRFCIZ-LTPNNWFFSA-N
Standard InCHI:	InChI=1S/C48H73N13O12/c1-26(23-27(2)37(73-7)24-31-13-9-8-10-14-31)17-18-32-28(3)40(64)59-35(45(69)70)19-20-39(63)61(6)30(5)42(66)55-29(4)41(65)58-34(16-12-22-54-48(51)52)44(68)60-36(46(71)72)25-38(62)56-33(43(67)57-32)15-11-21-53-47(49)50/h8-10,13-14,17-18,23,27-29,32-37H,5,11-12,15-16,19-22,24-25H2,1-4,6-7H3,(H,55,66)(H,56,62)(H,57,67)(H,58,65)(H,59,64)(H,60,68)(H,69,70)(H,71,72)(H4,49,50,53)(H4,51,52,54)/b18-17+,26-23+/t27-,28-,29+,32-,33-,34-,35+,36+,37-/m0/s1
SMILES:	CO[C@H]([C@H](/C=C(/C=C/[C@@H]1N=C(O)[C@H](CCCNC(=N)N)N=C(O)C[C@@H](N=C(O)[C@H](CCCNC(=N)N)N=C([C@H](N=C(C(=C)N(C(=O)CC[C@@H](N=C([C@H]1C)O)C(=O)O)C)O)C)O)C(=O)O)C)C)Cc1ccccc1
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL499276
PubChem CID:	21576447
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000264] Organic acids and derivatives [CHEMONTID:0001813] Peptidomimetics [CHEMONTID:0002010] Hybrid peptides

*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

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO32989	cyanobacterium planktothrixrubescens	Species	Cyanobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[15043406]

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☑ 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

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Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference
No data available in table

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☑ 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

Activity Type	# Activity
Others	1

Activity Type	# Activity
Others	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT2	Others	Unspecified	""	IC30	=	7.8	uM	PMID[533826]

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☑ 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 NPC24617 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	161
0.1-0.2	891
0.2-0.3	5356
0.3-0.4	19335
0.4-0.5	13817
0.5-0.6	2377
0.6-0.7	597
0.7-0.8	154
0.8-0.85	4
0.85-0.9	2
0.9-0.95	0
0.95-1	3

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Similarity Score	Similarity Level	Natural Product ID
0.9932	High Similarity	NPC114806
0.906	High Similarity	NPC300443
0.8125	Intermediate Similarity	NPC62104
0.8125	Intermediate Similarity	NPC1390
0.8065	Intermediate Similarity	NPC311658

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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 NPC24617 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	108
0.1-0.2	315
0.2-0.3	716
0.3-0.4	1783
0.4-0.5	4181
0.5-0.6	1823
0.6-0.7	204
0.7-0.8	17
0.8-0.85	3
0.85-0.9	0
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8523	High Similarity	NPD8076	Discontinued
0.8217	Intermediate Similarity	NPD6670	Clinical (unspecified phase)
0.8079	Intermediate Similarity	NPD6901	Phase 3
0.7862	Intermediate Similarity	NPD6078	Clinical (unspecified phase)
0.7771	Intermediate Similarity	NPD8303	Discontinued

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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