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Ligand clusters for UniProt code P0DTD1_5

Ligand clusters for P0DTD1_5: NSP5 - main protease (306 aa)

Top 6 (of 30) ligand clusters


Cluster 1. 210 ligand types 341 ligands		Cluster 2. 22 ligand types 57 ligands		Cluster 3. 10 ligand types 16 ligands		Cluster 4. 7 ligand types 7 ligands		Cluster 5. 9 ligand types 186 ligands		Cluster 6. 7 ligand types 43 ligands

Representative protein: 6xbiA

Structures

PDB		Schematic diagram

6xbiA
7cb7A
7abuA
7jq2A
7aqiA
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Cluster 1 contains 210 ligand types (of which only 20 are listed. Click for all)

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Ligand

Description

1. Ligand: DMS × 74

dimethyl sulfoxide

Dimethyl sulfoxide

PDB codes: 5r7y(A), 5r7z(A), 5r81(A), 5r82(A), 5re9(A), 5reh(A), 5rej(A), 5rep(A), 5ret(A), 5reu(A), 5rex(A), 5rf1(A), 5rf6(A), 5rfp(A), 5rfq(A), 5rfs(A), 5rfu(A), 5rfw(A), 5rfz(A), 5rg0(A), 5rg2(A), 5rg3(A), 5rgh(A), 5rgl(A), 5rgn(A), 5rgp(A), 5rgy(A), 5rh4(A), 5rhb(A), 5rhc(A), 5rhd(A), 5rhe(A), 6lze(A), 6m0k(A), 6y2f(A), 6yb7(A), 6yt8(A), 6yvf(A), 7a1u(A), 7abu(A), 7aga(A), 7amj(A), 7ans(A), 7aol(A), 7aqi(A), 7ar5(A), 7ar6(A), 7aws(A), 7aww(A), 7axm(A), 7axo(A), 7b83(A), 7buy(A), 7jr4(A), 7k3t(A), 7khp(A), 7mbg(A), 7mhf(A), 7mhg(A), 7mhh(A), 7mhi(A), 7mhk(A), 7mhl(A), 7mhm(A), 7mhn(A), 7mho(A), 7mng(A).

2. Ligand: SV6 × 6

telaprevir

(1s,3ar,6as)-2-[(2s)-2-({(2s)-2-Cyclohexyl-2-[(Pyrazin- 2-Ylcarbonyl)amino]acetyl}amino)-3,3-
Dimethylbutanoyl]-N-[(2r,3s)-1-(Cyclopropylamino)-2- Hydroxy-1-Oxohexan-3-
Yl]octahydrocyclopenta[c]pyrrole- 1-Carboxamide

PDB codes: 6xqs(A), 6zrt(A), 7c7p(A), 7k6d(A), 7k6e(A), 7lb7(A).

3. Ligand: GOL × 4

glycerin

Glycerol

PDB codes: 7cx9(A), 7ju7(A), 7l5d(A),

4. Ligand: ASC × 1

ascorbic acid

Ascorbic acid

PDB code: 7mpb(A).

5. Ligand: FUA × 1

fusidic acid

Fusidic acid

PDB code: 7a1u(A).

6. Ligand: G65 × 1

masitinib

Masitinib

PDB code: 7ju7(A).

7. Ligand: IPA × 1

isopropyl alcohol

Isopropyl alcohol

PDB code: 7nf5(A).

8. Ligand: SIN × 1

succinic acid

Succinic acid

PDB code: 7aha(A).

9. Ligand: EDO × 8

1,2-Ethanediol

PDB codes: 6xkf(A), 6xkh(A), 7b3e(A), 7bb2(A), 7be7(A), 7bgp(A), 7kyu(A).

10. Ligand: K36 × 7

(1s,2s)-2-({N-[(Benzyloxy)carbonyl]-L-Leucyl}amino)-1- Hydroxy-3-[(3s)-2-Oxopyrrolidin-3-
Yl]propane-1- Sulfonic acid

PDB codes: 6wtj(A), 6wtt(A), 7c6u(A), 7c8u(A), 7cb7(A), 7cbt(A), 7d1m(A).

11. Ligand: U5G × 7

Boceprevir (bound form)

PDB codes: 6wnp(A), 6xqu(A), 6zru(A), 7brp(B), 7c6s(A), 7com(A), 7k40(A).

12. Ligand: ALD × 5

N-[(Benzyloxy)carbonyl]-L-Leucyl-N-[(2s)-1-Hydroxy-4- Methylpentan-2-Yl]-L-Leucinamide

PDB codes: 7be7(A), 7bgp(A), 7nf5(A), 7ng3(A), 7ng6(A).

13. Ligand: ACE-LEU-LEU-AR7 × 4

ACE=Acetyl group, AR7=Amino{[(4s)-4-Amino-5,5- Dihydroxypentyl]amino}methaniminium.

PDB codes: 6xch(A), 6yz6(A), 7mrr(A), 7nev(A).

14. Ligand: UED × 4

N~2~-[(Benzyloxy)carbonyl]-N-{(2s)-1-Hydroxy-3-[(3s)-2- Oxopyrrolidin-3-Yl]propan-2-Yl}-L-
Leucinamide

PDB codes: 6wtk(A), 7jsu(A), 7lcp(A), 7lcq(A).

15. Ligand: NNA × 3

(1r,2s,5s)-3-[N-({1-[(Tert-Butylsulfonyl) methyl]cyclohexyl}carbamoyl)-3-Methyl-L-Valyl]-N- {(1s)-
1-[(1r)-2-(Cyclopropylamino)-1-Hydroxy-2- Oxoethyl]pentyl}-6,6-Dimethyl-3-
Azabicyclo[3.1.0]hexane-2-Carboxamide

PDB codes: 6xqt(A), 7d1o(A), 7jyc(A).

16. Ligand: TG3 × 3

Ethyl (4r)-4-[[(2s)-4-Methyl-2-[[(2s,3r)-3-[(2- Methylpropan-2-Yl)oxy]-2-
(Phenylmethoxycarbonylamino) butanoyl]amino]pentanoyl]amino]-5-[(3s)-2- Oxidanylidenepyrrolidin-3-
Yl]pentanoate

PDB codes: 7c8r(A), 7jt7(A), 7jw8(A).

17. Ligand: U88 × 3

5-Nitro-1,3-Thiazole

PDB codes: 7nby(A),

18. Ligand: 02J-ALA-VAL-LEU-PJE-010 × 2

02J=5-Methyl-1,2-Oxazole-3-Carboxylic acid, PJE=(E,4s)-4-Azanyl-5-[(3s)-2-Oxidanylidenepyrrolidin-3- Yl]pent-2-Enoic acid, 010=Phenylmethanol.

PDB codes: 6lu7(A), 7bqy(A).

19. Ligand: HF0 × 2

(2s,3s)-3,5-Dihydroxy-7-Methoxy-2-(3,4,5- Trihydroxyphenyl)chroman-4-One

PDB codes: 7dpv(A),

20. Ligand: IMD × 2

Imidazole

PDB codes: 7a1u(A), 7ax6(A).

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Cluster 2 contains 22 ligand types (of which only 20 are listed. Click for all)

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Ligand

Description

1. Ligand: DMS × 28

dimethyl sulfoxide

Dimethyl sulfoxide

PDB codes: 6yb7(A), 6yvf(A), 6yz6(A), 7a1u(A), 7abu(A), 7adw(A), 7aga(A), 7aha(A), 7amj(A), 7ans(A), 7aol(A), 7aqe(A), 7ar5(A), 7ar6(A), 7awr(A), 7aws(A), 7aww(A), 7axo(A), 7k3t(A), 7l5d(A), 7mng(A), 7mrr(A), 7nev(A).

2. Ligand: GOL × 3

glycerin

Glycerol

PDB codes: 6xbi(A), 7l5d(A), 7lyh(A).

3. Ligand: CLU × 1

clonidine

2,6-Dichloro-N-Imidazolidin-2-Ylideneaniline

PDB code: 7aww(A).

4. Ligand: S7W × 1

tegafur

Tegafur

PDB code: 7awr(A).

5. Ligand: IMD × 5

Imidazole

PDB codes: 7a1u(A), 7adw(A), 7aol(A), 7axm(A), 7ay7(A).

6. Ligand: MES × 2

2-(N-Morpholino)-Ethanesulfonic acid

PDB codes: 6w79(A), 6wco(A).

7. Ligand: NEN × 2

1-Ethyl-Pyrrolidine-2,5-Dione

PDB codes: 6xb1(A), 6xb2(A).

8. Ligand: HV2 × 1

1,1-Bis(oxidanylidene)thietan-3-Ol

PDB code: 5rf5(A).

9. Ligand: JJG × 1

4-[2-(Phenylsulfanyl)ethyl]morpholine

PDB code: 5red(A).

10. Ligand: K1G × 1

N,1-Dimethyl-N-(Propan-2-Yl)-1h-Pyrazolo[3,4- D]pyrimidin-4-Amine

PDB code: 5rgr(A).

11. Ligand: LWA × 1

(2~{s})-~{N}-(4-Aminocarbonylphenyl)oxolane-2- Carboxamide

PDB code: 5reg(A).

12. Ligand: PEG × 1

Di(hydroxyethyl)ether

PDB code: 7kvl(A).

13. Ligand: RQH × 1

(1~{s})-1-(4-Chloranylphenoxy)-1-Imidazol-1-Yl-3,3- Dimethyl-Butan-2-One

PDB code: 7aol(A).

14. Ligand: RVW × 1

(2~{s},3~{r},4~{r},5~{s},6~{s})-2-(Hydroxymethyl)-6- Sulfanyl-Oxane-3,4,5-Triol

PDB code: 7arf(A).

15. Ligand: S7D × 1

1-[(2~{s})-2-Methylmorpholin-4-Yl]-2-Pyrazol-1-Yl- Ethanone

PDB code: 5rf9(A).

16. Ligand: S8H × 1

(2~{s})-2-Azanyl-5-Oxidanylidene-5-[[(2~{s})-1- Oxidanylidene-1-[(2-Oxidanylidene-2-Propan-2-Yloxy-
Ethyl)amino]-3-Sulfanyl-Propan-2-Yl]amino]pentanoic acid

PDB code: 7ax6(A).

17. Ligand: T0V × 1

1-(3-Fluorophenyl)-N-[(Furan-2-Yl)methyl]methanamine

PDB code: 5re8(A).

18. Ligand: T1S × 1

4-[(3-Chlorophenyl)methyl]morpholine

PDB code: 5rei(A).

19. Ligand: T5Y × 1

Pyridin-2-Ol

PDB code: 5rf4(A).

20. Ligand: T6J × 1

2-[(Methylsulfonyl)methyl]-1h-Benzimidazole

PDB code: 5rfd(A).

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Cluster 3 contains 10 ligand types

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Ligand

Description

1. Ligand: GOL × 4

glycerin

Glycerol

PDB codes: 6xa4(A), 6xbh(A), 6xfn(A), 7lyi(A).

2. Ligand: DMS × 1

dimethyl sulfoxide

Dimethyl sulfoxide

PDB code: 7ax6(A).

3. Ligand: PEG × 4

Di(hydroxyethyl)ether

PDB codes: 6yvf(A), 7kfi(A), 7kvl(A), 7kvr(A).

4. Ligand: A82 × 1

2-[[(1r)-1-(7-Methyl-2-Morpholin-4-Yl-4-Oxidanylidene- Pyrido[1,2-A]pyrimidin-9-
Yl)ethyl]amino]benzoic acid

PDB code: 6yvf(A).

5. Ligand: K1Y × 1

Methyl (2-Methyl-4-Phenyl-1,3-Thiazol-5-Yl)carbamate

PDB code: 5rfc(A).

6. Ligand: K3S × 1

N-[(1-Methyl-1h-1,2,3-Triazol-4-Yl)methyl]ethanamine

PDB code: 5rfb(A).

7. Ligand: NZD × 1

4-Methyl-N-Phenylpiperazine-1-Carboxamide

PDB code: 5rgg(A).

8. Ligand: O0S × 1

N-{4-[(Pyrimidin-2-Yl)oxy]phenyl}acetamide

PDB code: 5re6(A).

9. Ligand: T0J × 1

N~1~-Phenylpiperidine-1,4-Dicarboxamide

PDB code: 5re5(A).

10. Ligand: UHG × 1

(2r)-2-(6-Chloro-9h-Carbazol-2-Yl)propanoic acid

PDB code: 5rh4(A).

Cluster 4 contains 7 ligand types

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Ligand

Description

1. Ligand: QEL × 1

ifenprodil

4-[(1r,2s)-2-(4-Benzylpiperidin-1-Yl)-1- Hydroxypropyl]phenol

PDB code: 7aqi(A).

2. Ligand: 93J × 1

(2e)-N-{4-[(3-Chloro-4-Fluorophenyl)amino]-3-Cyano-7- Ethoxyquinolin-6-Yl}-4-(Dimethylamino)but-2-
Enamide

PDB code: 7axm(A).

3. Ligand: ACT × 1

Acetate ion

PDB code: 7ng6(A).

4. Ligand: EDO × 1

1,2-Ethanediol

PDB code: 7be7(A).

5. Ligand: R6Q × 1

1'-[2-[4-(Trifluoromethyl)phenyl]ethyl]spiro[1~{h}-3,1- Benzoxazine-4,4'-Piperidine]-2-One

PDB code: 7abu(A).

6. Ligand: RMZ × 1

(3~{s})-3-[2-[4-(3,4-Dimethylphenyl)piperazin-1- Yl]ethyl]-2,3-Dihydroisoindol-1-One

PDB code: 7amj(A).

7. Ligand: U88 × 1

5-Nitro-1,3-Thiazole

PDB code: 7nby(A).

Cluster 5 contains 9 ligand types

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Ligand

Description

1. Ligand: DMS × 173

dimethyl sulfoxide

Dimethyl sulfoxide

PDB codes: 5r7y(A), 5r7z(A), 5r80(A), 5r81(A), 5r82(A), 5r83(A), 5r84(A), 5r8t(A), 5re4(A), 5re5(A), 5re6(A), 5re7(A), 5re8(A), 5re9(A), 5rea(A), 5reb(A), 5rec(A), 5red(A), 5ree(A), 5ref(A), 5reg(A), 5reh(A), 5rei(A), 5rej(A), 5rek(A), 5rel(A), 5rem(A), 5ren(A), 5reo(A), 5rep(A), 5rer(A), 5res(A), 5ret(A), 5reu(A), 5rev(A), 5rew(A), 5rex(A), 5rey(A), 5rez(A), 5rf0(A), 5rf1(A), 5rf2(A), 5rf3(A), 5rf4(A), 5rf5(A), 5rf6(A), 5rf7(A), 5rf8(A), 5rf9(A), 5rfb(A), 5rfc(A), 5rfd(A), 5rfe(A), 5rff(A), 5rfg(A), 5rfh(A), 5rfi(A), 5rfj(A), 5rfk(A), 5rfl(A), 5rfm(A), 5rfn(A), 5rfo(A), 5rfp(A), 5rfq(A), 5rfr(A), 5rfs(A), 5rft(A), 5rfu(A), 5rfv(A), 5rfw(A), 5rfx(A), 5rfy(A), 5rfz(A), 5rg0(A), 5rg1(A), 5rg2(A), 5rg3(A), 5rgg(A), 5rgh(A), 5rgi(A), 5rgj(A), 5rgk(A), 5rgl(A), 5rgm(A), 5rgn(A), 5rgo(A), 5rgp(A), 5rgs(A), 5rgt(A), 5rgu(A), 5rgv(A), 5rgw(A), 5rgx(A), 5rgy(A), 5rgz(A), 5rh0(A), 5rh1(A), 5rh2(A), 5rh3(A), 5rh4(A), 5rh5(A), 5rh6(A), 5rh7(A), 5rh8(A), 5rh9(A), 5rha(A), 5rhb(A), 5rhc(A), 5rhd(A), 5rhe(A), 5rhf(A), 5rl0(A), 5rl1(A), 5rl2(A), 5rl3(A), 5rl4(A), 5rl5(A), 6lze(A), 6m0k(A), 6xb0(A), 6xb2(A), 6yb7(A), 6zrt(A), 6zru(A), 7a1u(A), 7abu(A), 7adw(A), 7aga(A), 7aha(A), 7amj(A), 7ans(A), 7aol(A), 7ar5(A), 7ar6(A), 7arf(A), 7awr(A), 7aws(A), 7aww(A), 7axm(A), 7axo(A), 7ay7(A), 7buy(A), 7jr4(A), 7jyc(A), 7k3t(A), 7k40(A), 7k6d(A), 7k6e(A), 7kfi(A), 7kfj(A), 7khp(A), 7ks5(A), 7kvl(A), 7kvr(A), 7kw5(A), 7l5d(A), 7ldx(A), 7lfe(A), 7lfp(A), 7mbg(A), 7mhf(A), 7mhg(A), 7mhh(A), 7mhi(A), 7mhk(A), 7mhl(A), 7mhm(A), 7mhn(A), 7mhq(A), 7mng(A), 7nev(A).

2. Ligand: GLY × 1

glycine

PDB code: 6y2g(A).

3. Ligand: EDO × 6

1,2-Ethanediol

PDB codes: 7be7(A), 7bgp(A), 7lcp(A), 7lcq(A), 7nf5(A).

4. Ligand: 6SU × 1

Methyl 3-(Methylsulfonylamino)benzoate

PDB code: 5ref(A).

5. Ligand: IMD × 1

Imidazole

PDB code: 7aqi(A).

6. Ligand: JGY × 1

1-Methyl-N-{[(2s)-Oxolan-2-Yl]methyl}-1h-Pyrazole-3- Carboxamide

PDB code: 5rfa(A).

7. Ligand: LZE × 1

4-{[(2,6-Dichlorophenyl)carbonyl]amino}-N-Piperidin-4- Yl-1h-Pyrazole-3-Carboxamide

PDB code: 7aga(A).

8. Ligand: PEG × 1

Di(hydroxyethyl)ether

PDB code: 6yt8(A).

9. Ligand: U1V × 1

1-(4-Fluoro-2-Methylphenyl)methanesulfonamide

PDB code: 5rgq(A).

Cluster 6 contains 7 ligand types

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Ligand

Description

1. Ligand: DMS × 34

dimethyl sulfoxide

Dimethyl sulfoxide

PDB codes: 5rec(A), 5rgt(A), 5rgu(A), 5rgv(A), 5rgw(A), 5rgx(A), 5rgy(A), 5rgz(A), 5rh0(A), 5rh1(A), 5rh2(A), 5rh4(A), 5rh5(A), 5rh6(A), 5rh7(A), 5rh8(A), 5rh9(A), 5rha(A), 5rhb(A), 5rhc(A), 5rhd(A), 5rhe(A), 5rhf(A), 5rl0(A), 5rl1(A), 5rl2(A), 5rl3(A), 5rl4(A), 5rl5(A), 6yb7(A), 7aga(A), 7aha(A), 7k3t(A), 7mhg(A).