Protein profile

KP13_03545

Cysteine synthase B

Genome: KpKP13

Gene: AHE43351.1 cysM Structure source: AlphaFold + ColabFold UniProt A0A0H3GRE2

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Amino acids 303

Annotations 3

Features 18

PDB binders 8

Druggability 0.904

Overview

Basic information about this protein and its source genome.

Accession: KP13_03545
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE43351.1 cysM
Status: annotated
Amino acids: 303
Structure source: AlphaFold + ColabFold

2.5.1.47

GO:0006535 OBSOLETE. The chemical reactions and pathways resulting in the formation of cysteine from L- serine. GO:0004124 Catalysis of the reaction: O3-acetyl-L-serine + hydrogen sulfide = L-cysteine + acetate.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 48.958
Human E-value: 1.31e-23
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 64.189
DEG E-value: 7.619999999999999e-134
Localization: Cytoplasmic
ColabFold pLDDT: 94.55

Selected Druggability evidence

AlphaFold / UniProt model

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.

FPocket 0.904

Structure A0A0H3GRE2

Pocket Pocket 2

P2Rank 0.877

Structure A0A0H3GRE2

Pocket Pocket 1

ColabFold model

FPocket 0.44 · Pocket 8

P2Rank 0.933 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 157 / 4744 genomes with a hit

Normalized 0.033

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 2 GO

Enzyme Commission (EC)

2.5.1.47

Gene Ontology (GO)

GO:0006535 OBSOLETE. The chemical reactions and pathways resulting in the formation of cysteine from L- serine.
GO:0004124 Catalysis of the reaction: O3-acetyl-L-serine + hydrogen sulfide = L-cysteine + acetate.

Sequence Features

Domain/signature hits from InterPro and related databases.

18 records

Show feature table

Start	End	DB	Term	Name
3	289	SUPERFAMILY	SSF53686	Tryptophan synthase beta subunit-like PLP-dependent enzymes
3	289	InterPro	IPR036052	Tryptophan synthase beta chain-like, PALP domain superfamily
5	292	NCBIfam	TIGR01136	cysteine synthase
5	292	InterPro	IPR005856	Cysteine synthase
38	147	FunFam	G3DSA:3.40.50.1100:FF:000003	Cystathionine beta-synthase
5	281	Pfam	PF00291	Pyridoxal-phosphate dependent enzyme
5	281	InterPro	IPR001926	Tryptophan synthase beta chain-like, PALP domain
9	288	CDD	cd01561	CBS_like
148	289	FunFam	G3DSA:3.40.50.1100:FF:000029	Cysteine synthase
30	48	ProSitePatterns	PS00901	Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site.
30	48	InterPro	IPR001216	Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site
7	289	Gene3D	G3DSA:3.40.50.1100	-
7	289	InterPro	IPR036052	Tryptophan synthase beta chain-like, PALP domain superfamily
5	293	PANTHER	PTHR10314	CYSTATHIONINE BETA-SYNTHASE
3	292	NCBIfam	TIGR01138	cysteine synthase B
3	292	InterPro	IPR005858	Cysteine synthase CysM
35	140	Gene3D	G3DSA:3.40.50.1100	-
35	140	InterPro	IPR036052	Tryptophan synthase beta chain-like, PALP domain superfamily

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

Loading 3D structure...

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Structural evidence

0 + 2

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold AF_A0A0H3GRE2	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_03545	ColabFold	—	—	full sequence	—	Loaded

Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET	Sticks	Spheres	Surfaces	Druggability	Labels	Zoom	Positions
2				0.904

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				13.87	0.702
2				2.55	0.072

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET	Sticks	Spheres	Surfaces	Druggability	Labels	Zoom	Positions
8				0.44

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				19.09	0.834
2				2.3	0.058

Ligand evidence

Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.

73 records

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in TPW, use Open crystal to inspect it in the structure viewer.

No PDB structure with a co-crystallized ligand found for this exact protein.

Structural evidence inferred from similar proteins. The source crystal indicates where the ligand was observed; the UniProt column identifies the homologous protein carrying that ligand.

Ligand	Source crystal	UniProt (homolog)	MW · LogP · TPSA	Lipinski	PAINS	SMILES
3HL	2ECQ	Q5SLE6	104.1 Da LogP -0.16 TPSA 57.5	✓ Ro5	✓ Clean	`C[C@@H](CC(=O)O)O`
4AT	2EFY	Q5SLE6	130.1 Da LogP 0.83 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)CCCC(=O)O`
4MV	2ECO	Q5SLE6	116.2 Da LogP 1.51 TPSA 37.3	✓ Ro5	✓ Clean	`CC(C)CCC(=O)O`
AA5	1Z7Y	P47998	378.3 Da LogP 1.33 TPSA 149.5	✓ Ro5	✓ Clean	`Cc1c(c(c(cn1)COP(=O)(O)O)C=N[C@@H](CCSC)C(=O)O)O`
AWH	3ZEI	P9WP55	412.4 Da LogP 3.08 TPSA 116.5	✓ Ro5	✓ Clean	`CN\1C(=O)/C(=C/c2ccccc2OCC(=O)O)/S/C1=N\c3cccc(…`
C6P	3VC3	I1L6I6	352.3 Da LogP 0.18 TPSA 149.2	1 viol.	✓ Clean	`Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H](CS)C(=O)O)O`
PDA	2Q3D	P9WP55	320.2 Da LogP 0.27 TPSA 149.2	✓ Ro5	✓ Clean	`Cc1c(c(c(cn1)COP(=O)(O)O)CNC(C)C(=O)O)O`
PUS	3X44	D2Z027	392.3 Da LogP -0.82 TPSA 213.9	1 viol.	✓ Clean	`Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/[C@@H](CONC(=O)N)…`

Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL bioactivity data found for this exact protein.

Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
CHEMBL2418481	P9WP55	7.72	356.4 Da LogP 3.76 TPSA 70.0	✓ Ro5	✓ Clean	`CN1C(=O)/C(=C/c2ccc(F)cc2)S/C1=N\c1cccc(C(=O)O)…`
CHEMBL2418529	P9WP55	7.59	444.5 Da LogP 5.20 TPSA 79.2	1 viol.	✓ Clean	`CN1C(=O)/C(=C/c2ccc(OCc3ccccc3)cc2)S/C1=N\c1ccc…`
CHEMBL2418524	P9WP55	7.47	368.4 Da LogP 3.63 TPSA 79.2	✓ Ro5	✓ Clean	`COc1ccc(/C=C2\S/C(=N\c3cccc(C(=O)O)c3)N(C)C2=O)…`
CHEMBL2418487	P9WP55	7.43	381.5 Da LogP 3.68 TPSA 73.2	✓ Ro5	Alert	`CN1C(=O)/C(=C/c2ccc(N(C)C)cc2)S/C1=N\c1cccc(C(=…`
CHEMBL2418504	P9WP55	7.26	398.4 Da LogP 3.64 TPSA 88.4	✓ Ro5	✓ Clean	`COc1ccc(/C=C2\S/C(=N\c3cccc(C(=O)O)c3)N(C)C2=O)…`
CHEMBL2418505	P9WP55	7.25	412.5 Da LogP 4.03 TPSA 88.4	✓ Ro5	✓ Clean	`CCN1C(=O)/C(=C/c2ccc(OC)c(OC)c2)S/C1=N\c1cccc(C…`
CHEMBL2418502	P9WP55	7.22	384.4 Da LogP 3.33 TPSA 99.4	✓ Ro5	✓ Clean	`COc1cc(/C=C2\S/C(=N\c3cccc(C(=O)O)c3)N(C)C2=O)c…`
CHEMBL2418568	P9WP55	7.20	354.4 Da LogP 3.32 TPSA 90.2	✓ Ro5	✓ Clean	`CN1C(=O)/C(=C/c2ccc(O)cc2)S/C1=N\c1cccc(C(=O)O)…`
CHEMBL2418489	P9WP55	7.16	428.5 Da LogP 3.64 TPSA 97.7	✓ Ro5	✓ Clean	`COc1cc(/C=C2\S/C(=N\c3cccc(C(=O)O)c3)N(C)C2=O)c…`
CHEMBL2418545	P9WP55	7.02	382.4 Da LogP 4.10 TPSA 90.2	✓ Ro5	✓ Clean	`CCCN1C(=O)/C(=C/c2ccc(O)cc2)S/C1=N\c1cccc(C(=O)…`
CHEMBL2418569	P9WP55	6.99	368.4 Da LogP 3.71 TPSA 90.2	✓ Ro5	✓ Clean	`CCN1C(=O)/C(=C/c2ccc(O)cc2)S/C1=N\c1cccc(C(=O)O…`
CHEMBL2418548	P9WP55	6.96	380.4 Da LogP 3.88 TPSA 90.2	✓ Ro5	✓ Clean	`C=CCN1C(=O)/C(=C/c2ccc(O)cc2)S/C1=N\c1cccc(C(=O…`
CHEMBL2418551	P9WP55	6.85	382.4 Da LogP 4.10 TPSA 90.2	✓ Ro5	✓ Clean	`CC(C)N1C(=O)/C(=C/c2ccc(O)cc2)S/C1=N\c1cccc(C(=…`
CHEMBL2418514	P9WP55	6.79	368.4 Da LogP 3.63 TPSA 79.2	✓ Ro5	✓ Clean	`COc1ccccc1/C=C1\S/C(=N\c2cccc(C(=O)O)c2)N(C)C1=O`
CHEMBL4858734	P9WP55	6.20	844.9 Da LogP 1.49 TPSA 257.4	3 viol.	Alert	`C[C@@H]1O[C@@H](O[C@@H]2C[C@H](c3ccc4c(c3O)C(=O…`

Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).

Ligand	Tanimoto	MW · LogP · TPSA	Lipinski	PAINS	SMILES
ZINC100260795	1.000	412.4 Da LogP 3.08 TPSA 116.5	✓ Ro5	✓ Clean	`CN1C(=O)/C(=C/c2ccccc2OCC(=O)O)S/C1=N/c1cccc(C(…`
ZINC4575663	1.000	398.4 Da LogP 3.64 TPSA 88.4	✓ Ro5	✓ Clean	`COc1ccc(/C=C2\S/C(=N/c3cccc(C(=O)O)c3)N(C)C2=O)…`
ZINC4599096	1.000	384.4 Da LogP 3.33 TPSA 99.4	✓ Ro5	✓ Clean	`COc1cc(/C=C2\S/C(=N/c3cccc(C(=O)O)c3)N(C)C2=O)c…`
ZINC5065718	1.000	381.5 Da LogP 3.68 TPSA 73.2	✓ Ro5	Alert	`CN1C(=O)/C(=C/c2ccc(N(C)C)cc2)S/C1=N/c1cccc(C(=…`
ZINC100321212	0.867	398.4 Da LogP 3.72 TPSA 99.4	✓ Ro5	✓ Clean	`CCN1C(=O)/C(=C/c2ccc(OC)c(O)c2)S/C1=N/c1cccc(C(…`
ZINC100936755	0.867	398.4 Da LogP 3.72 TPSA 99.4	✓ Ro5	✓ Clean	`CCN1C(=O)/C(=C/c2ccc(O)c(OC)c2)S/C1=N/c1cccc(C(…`
ZINC33684545	0.867	398.4 Da LogP 3.72 TPSA 99.4	✓ Ro5	✓ Clean	`CCN1C(=O)/C(=C\c2ccc(O)c(OC)c2)S/C1=N\c1cccc(C(…`
ZINC100260846	0.862	384.4 Da LogP 3.33 TPSA 99.4	✓ Ro5	✓ Clean	`COc1ccc(/C=C2\S/C(=N/c3cccc(C(=O)O)c3)N(C)C2=O)…`
ZINC4660262	0.860	382.4 Da LogP 3.94 TPSA 79.2	✓ Ro5	✓ Clean	`COc1ccc(/C=C2\S/C(=N/c3cccc(C(=O)O)c3)N(C)C2=O)…`
ZINC100309209	0.852	461.3 Da LogP 4.78 TPSA 79.2	✓ Ro5	✓ Clean	`CCN1C(=O)/C(=C/c2ccc(OC)c(Br)c2)S/C1=N/c1cccc(C…`
ZINC6878883	0.850	442.4 Da LogP 3.09 TPSA 125.7	✓ Ro5	✓ Clean	`COc1cc(/C=C2\S/C(=N/c3cccc(C(=O)O)c3)N(C)C2=O)c…`
ZINC100318601	0.845	402.9 Da LogP 4.28 TPSA 79.2	✓ Ro5	✓ Clean	`COc1ccc(/C=C2\S/C(=N/c3cccc(C(=O)O)c3)N(C)C2=O)…`
ZINC100928204	0.845	447.3 Da LogP 4.39 TPSA 79.2	✓ Ro5	✓ Clean	`COc1ccc(/C=C2\S/C(=N/c3cccc(C(=O)O)c3)N(C)C2=O)…`
ZINC8438503	0.845	494.3 Da LogP 4.23 TPSA 79.2	✓ Ro5	✓ Clean	`COc1ccc(/C=C2\S/C(=N/c3cccc(C(=O)O)c3)N(C)C2=O)…`
ZINC100318659	0.844	436.5 Da LogP 4.03 TPSA 88.4	✓ Ro5	✓ Clean	`C#CCOc1ccc(/C=C2\S/C(=N/c3cccc(C(=O)O)c3)N(CC)C…`
ZINC100260861	0.840	338.4 Da LogP 3.62 TPSA 70.0	✓ Ro5	✓ Clean	`CN1C(=O)/C(=C/c2ccccc2)S/C1=N/c1cccc(C(=O)O)c1`
ZINC8642766	0.840	338.4 Da LogP 3.62 TPSA 70.0	✓ Ro5	✓ Clean	`CN1C(=O)/C(=C/c2ccccc2)S/C1=N\c1cccc(C(=O)O)c1`
ZINC4698831	0.836	368.4 Da LogP 3.63 TPSA 79.2	✓ Ro5	✓ Clean	`COc1cccc(/C=C2/S/C(=N\c3cccc(C(=O)O)c3)N(C)C2=O…`
ZINC14619253	0.833	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)CCCCCCCCCC(=O)O`
ZINC1841307	0.833	228.3 Da LogP 3.56 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)CCCCCCCCCCC(=O)O`
ZINC1845839	0.833	200.3 Da LogP 2.78 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)CCCCCCCCC(=O)O`
ZINC33822328	0.833	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)CCCCCCCCCCCCCC(=O)O`
ZINC5855130	0.833	242.4 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)CCCCCCCCCCCC(=O)O`
ZINC83316693	0.828	412.4 Da LogP 3.08 TPSA 116.5	✓ Ro5	✓ Clean	`CN1C(=O)/C(=C/c2ccccc2OCC(=O)O)S/C1=N/c1ccc(C(=…`
ZINC100309361	0.827	354.4 Da LogP 3.32 TPSA 90.2	✓ Ro5	✓ Clean	`CN1C(=O)/C(=C/c2ccc(O)cc2)S/C1=N/c1cccc(C(=O)O)…`
ZINC2296453232	0.827	354.4 Da LogP 3.32 TPSA 90.2	✓ Ro5	✓ Clean	`CN1C(=O)C(=Cc2ccc(O)cc2)SC1=Nc1cccc(C(=O)O)c1`
ZINC5024864	0.827	352.4 Da LogP 3.93 TPSA 70.0	✓ Ro5	✓ Clean	`Cc1ccc(/C=C2\S/C(=N/c3cccc(C(=O)O)c3)N(C)C2=O)c…`
ZINC6878881	0.825	428.5 Da LogP 3.64 TPSA 97.7	✓ Ro5	✓ Clean	`COc1cc(/C=C2\S/C(=N/c3cccc(C(=O)O)c3)N(C)C2=O)c…`
ZINC100927880	0.820	491.3 Da LogP 3.84 TPSA 116.5	✓ Ro5	✓ Clean	`CN1C(=O)/C(=C/c2cc(Br)ccc2OCC(=O)O)S/C1=N/c1ccc…`
ZINC4591268	0.820	398.4 Da LogP 3.72 TPSA 99.4	✓ Ro5	✓ Clean	`CCOc1cc(/C=C2\S/C(=N/c3cccc(C(=O)O)c3)N(C)C2=O)…`
ZINC100260791	0.817	412.4 Da LogP 3.08 TPSA 116.5	✓ Ro5	✓ Clean	`CN1C(=O)/C(=C/c2ccc(OCC(=O)O)cc2)S/C1=N/c1cccc(…`
ZINC100260761	0.811	372.8 Da LogP 4.27 TPSA 70.0	✓ Ro5	✓ Clean	`CN1C(=O)/C(=C/c2ccc(Cl)cc2)S/C1=N/c1cccc(C(=O)O…`
ZINC8642746	0.811	372.8 Da LogP 4.27 TPSA 70.0	✓ Ro5	✓ Clean	`CN1C(=O)/C(=C/c2ccc(Cl)cc2)S/C1=N\c1cccc(C(=O)O…`
ZINC100927270	0.810	384.4 Da LogP 3.33 TPSA 99.4	✓ Ro5	✓ Clean	`COc1cc(/C=C2\S/C(=N/c3ccc(C(=O)O)cc3)N(C)C2=O)c…`
ZINC6878882	0.810	422.5 Da LogP 3.64 TPSA 88.4	✓ Ro5	✓ Clean	`C#CCOc1ccc(/C=C2\S/C(=N/c3cccc(C(=O)O)c3)N(C)C2…`
ZINC100260755	0.807	368.4 Da LogP 3.63 TPSA 79.2	✓ Ro5	✓ Clean	`COc1ccccc1/C=C1\S/C(=N/c2cccc(C(=O)O)c2)N(C)C1=O`
ZINC1007728	0.804	396.4 Da LogP 3.41 TPSA 96.3	✓ Ro5	✓ Clean	`COC(=O)c1ccc(/C=C2\S/C(=N/c3cccc(C(=O)O)c3)N(C)…`
ZINC4680392	0.804	340.4 Da LogP 3.63 TPSA 62.1	✓ Ro5	✓ Clean	`COc1cc(/C=C2/S/C(=N/c3ccccc3)N(C)C2=O)ccc1O`
ZINC97456580	0.804	398.4 Da LogP 3.64 TPSA 88.4	✓ Ro5	✓ Clean	`COc1ccc(/C=C2\S/C(=N/c3ccc(C(=O)O)cc3)N(C)C2=O)…`
ZINC4466315	0.792	336.4 Da LogP 4.18 TPSA 52.9	✓ Ro5	✓ Clean	`C=CCN1C(=O)/C(=C\c2ccc(O)cc2)S/C1=N/c1ccccc1`
ZINC100937907	0.790	488.5 Da LogP 4.90 TPSA 116.5	✓ Ro5	✓ Clean	`CN1C(=O)/C(=C/c2ccccc2OCc2ccc(C(=O)O)cc2)S/C1=N…`
ZINC4664355	0.789	368.5 Da LogP 4.33 TPSA 51.1	✓ Ro5	✓ Clean	`CCN1C(=O)/C(=C\c2ccc(OC)c(OC)c2)S/C1=N/c1ccccc1`
ZINC4698651	0.789	398.4 Da LogP 3.64 TPSA 88.4	✓ Ro5	✓ Clean	`COc1ccc(OC)c(/C=C2/S/C(=N\c3cccc(C(=O)O)c3)N(C)…`
ZINC8399628	0.783	426.5 Da LogP 4.42 TPSA 88.4	✓ Ro5	✓ Clean	`CCOc1ccc(/C=C2\S/C(=N/c3cccc(C(=O)O)c3)N(C)C2=O…`
ZINC5033940	0.782	380.5 Da LogP 4.74 TPSA 70.0	✓ Ro5	✓ Clean	`CC(C)c1ccc(/C=C2\S/C(=N/c3cccc(C(=O)O)c3)N(C)C2…`
ZINC100215266	0.778	381.5 Da LogP 3.68 TPSA 73.2	✓ Ro5	Alert	`CN1C(=O)/C(=C/c2ccc(N(C)C)cc2)S/C1=N/c1ccc(C(=O…`
ZINC5558020	0.778	368.4 Da LogP 3.63 TPSA 79.2	✓ Ro5	✓ Clean	`COc1ccc(/C=C2\S/C(=N/c3ccc(C(=O)O)cc3)N(C)C2=O)…`
ZINC100260866	0.776	398.4 Da LogP 3.64 TPSA 88.4	✓ Ro5	✓ Clean	`COc1ccc(/C=C2\S/C(=N/c3cccc(C(=O)O)c3)N(C)C2=O)…`
ZINC4691610	0.776	382.4 Da LogP 3.94 TPSA 79.2	✓ Ro5	✓ Clean	`COc1ccc(/C=C2/S/C(=N\c3cccc(C(=O)O)c3)N(C)C2=O)…`
ZINC100311577	0.769	491.4 Da LogP 4.79 TPSA 88.4	✓ Ro5	✓ Clean	`CCN1C(=O)/C(=C/c2cc(Br)c(OC)c(OC)c2)S/C1=N/c1cc…`

PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.