Protein profile

VK055_1181

cysB

Genome: KpATCC43816

Gene: AIK79804.1 cysB Structure source: Experimental + ColabFold UniProt P45600

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Amino acids 324

Annotations 5

Features 23

PDB binders 8

Druggability 0.487

Overview

Basic information about this protein and its source genome.

Accession: VK055_1181
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK79804.1 cysB
Status: annotated
Amino acids: 324
Structure source: Experimental + ColabFold

GO:0003700 A transcription regulator activity that modulates transcription of gene sets via selective and non-covalent binding to a specific double-stranded genomic DNA sequence (sometimes referred to as a motif) within a cis-regulatory region. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons. GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0000976 Binding to a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon. GO:0019344 The chemical reactions and pathways resulting in the formation of L-cysteine, 2-amino-3-mercaptopropanoic acid.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 95.37
DEG E-value: 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 93.07

Selected Druggability evidence

PDB experimental structure

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 0.487

Structure 9FDD

Pocket Pocket 14

P2Rank 0.331

Structure 9F14

Pocket Pocket 1

ColabFold model

FPocket 0.388 · Pocket 13

P2Rank 0.362 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 154 / 4744 genomes with a hit

Normalized 0.032

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

GO:0003700 A transcription regulator activity that modulates transcription of gene sets via selective and non-covalent binding to a specific double-stranded genomic DNA sequence (sometimes referred to as a motif) within a cis-regulatory region. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons.
GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0000976 Binding to a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon.
GO:0019344 The chemical reactions and pathways resulting in the formation of L-cysteine, 2-amino-3-mercaptopropanoic acid.

Sequence Features

Domain/signature hits from InterPro and related databases.

23 records

Show feature table

Start	End	DB	Term	Name
167	267	Gene3D	G3DSA:3.40.190.10	-
1	59	ProSiteProfiles	PS50931	LysR-type HTH domain profile.
1	59	InterPro	IPR000847	Transcription regulator HTH, LysR
3	64	Pfam	PF00126	Bacterial regulatory helix-turn-helix protein, lysR family
3	64	InterPro	IPR000847	Transcription regulator HTH, LysR
1	85	SUPERFAMILY	SSF46785	Winged helix DNA-binding domain
1	85	InterPro	IPR036390	Winged helix DNA-binding domain superfamily
1	87	Gene3D	G3DSA:1.10.10.10	-
1	87	InterPro	IPR036388	Winged helix-like DNA-binding domain superfamily
1	297	PANTHER	PTHR30126	HTH-TYPE TRANSCRIPTIONAL REGULATOR
1	89	FunFam	G3DSA:1.10.10.10:FF:000021	HTH-type transcriptional regulator CysB
19	30	PRINTS	PR00039	LysR bacterial regulatory protein HTH signature
19	30	InterPro	IPR000847	Transcription regulator HTH, LysR
30	40	PRINTS	PR00039	LysR bacterial regulatory protein HTH signature
30	40	InterPro	IPR000847	Transcription regulator HTH, LysR
40	51	PRINTS	PR00039	LysR bacterial regulatory protein HTH signature
40	51	InterPro	IPR000847	Transcription regulator HTH, LysR
92	292	Pfam	PF03466	LysR substrate binding domain
92	292	InterPro	IPR005119	LysR, substrate-binding
91	303	Gene3D	G3DSA:3.40.190.10	-
91	322	SUPERFAMILY	SSF53850	Periplasmic binding protein-like II
94	291	CDD	cd08443	PBP2_CysB
167	267	FunFam	G3DSA:3.40.190.10:FF:000037	HTH-type transcriptional regulator CysB

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

3 + 1

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

Entry	Method	Resolution	Chain	Coverage	Links	Status
PDB 1AL3	X-ray	1.80 Å	A	100.0% 1-324	PDBe RCSB PDBj File	Viewing
PDB 9F14	X-ray	2.30 Å	A,B	100.0% 1-324	PDBe RCSB PDBj File	Loaded
PDB 9FDD	X-ray	2.80 Å	A,B,C,D,E,F,G,H	100.0% 1-324	PDBe RCSB PDBj File	Loaded
ColabFold VK055_1181	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
4				0.258

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	Score	Probability
1	1.5	0.021
2	1.46	0.02
3	1.46	0.02

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
13				0.388
11				0.367

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				5.53	0.264
2				0.96	0.005

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.

58 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
1PS	6G1B	Q8NP91	201.2 Da LogP -0.09 TPSA 61.1	✓ Ro5	✓ Clean	`c1cc[n+](cc1)CCCS(=O)(=O)[O-]`
AKG	5Y2V	P73862	146.1 Da LogP -0.50 TPSA 91.7	✓ Ro5	✓ Clean	`C(CC(=O)O)C(=O)C(=O)O`
FOR	6G1D	Q8NP91	30.0 Da LogP -0.18 TPSA 17.1	✓ Ro5	✓ Clean	`C=O`
OAS	4LQ2	P06614	147.1 Da LogP -1.04 TPSA 89.6	✓ Ro5	✓ Clean	`CC(=O)OC[C@@H](C(=O)O)N`
PEO	6G1B	Q8NP91	34.0 Da LogP 0.02 TPSA 40.5	✓ Ro5	✓ Clean	`OO`
RUB	5Z49	Q9F1R2	310.1 Da LogP -2.50 TPSA 191.0	1 viol.	✓ Clean	`C([C@H]([C@H](C(=O)COP(=O)(O)O)O)O)OP(=O)(O)O`
SAC	4M4G	P06614	147.1 Da LogP -1.43 TPSA 86.6	✓ Ro5	✓ Clean	`CC(=O)N[C@@H](CO)C(=O)O`
SKM	5TED	Q8Y9N7	174.2 Da LogP -1.52 TPSA 98.0	✓ Ro5	✓ Clean	`C1[C@H]([C@@H]([C@@H](C=C1C(=O)O)O)O)O`

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).

No ChEMBL hits found through similar proteins.

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
ZINC3870277	1.000	310.1 Da LogP -2.50 TPSA 191.0	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC12502210	0.793	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@H](O)[C@@H](O)COP(=O…`
ZINC12502212	0.793	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@H](O)[C@H](O)COP(=O)…`
ZINC12502214	0.793	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@@H](O)[C@@H](O)COP(=…`
ZINC12502216	0.793	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@@H](O)[C@H](O)COP(=O…`
ZINC4523251	0.793	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@@H](O)[C@@H](O)[C@@H](O)COP(…`
ZINC4523255	0.793	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@@H](O)[C@@H](O)[C@H](O)COP(=…`
ZINC4523257	0.793	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@@H](O)[C@H](O)[C@@H](O)COP(=…`
ZINC4523259	0.793	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@@H](O)[C@H](O)[C@H](O)COP(=O…`
ZINC1529626	0.724	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@H](O)[C@@H](O)COP(=O)(O)O`
ZINC1532567	0.724	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC1532851	0.724	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@@H](O)[C@@H](O)COP(=O)(O)O`
ZINC30320708	0.724	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC31259596	0.724	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(COP(=O)(O)O)[C@@H](O)[C@H](O)CO`
ZINC31259600	0.724	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(COP(=O)(O)O)[C@@H](O)[C@@H](O)CO`
ZINC3869804	0.724	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@@H](O)CO`
ZINC3869805	0.724	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@H](O)CO`
ZINC1560408815	0.656	339.1 Da LogP -1.87 TPSA 214.1	1 viol.	✓ Clean	`[O]/C(COP(=O)(O)O)=C(/O)[C@H](O)[C@H](O)COP(=O)…`
ZINC5830339	0.645	231.1 Da LogP -2.68 TPSA 156.5	1 viol.	✓ Clean	`O=C(NO)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC4521819	0.643	202.3 Da LogP 0.25 TPSA 58.3	✓ Ro5	✓ Clean	`O=S(=O)(O)CCC[n+]1ccccc1`
ZINC18140538	0.625	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@@H](O)[C@H](O)[C@H](O)CO`
ZINC100029384	0.594	244.1 Da LogP -2.23 TPSA 144.5	✓ Ro5	✓ Clean	`C[C@H](O)[C@@H](O)[C@@H](O)C(=O)COP(=O)(O)O`
ZINC1602740	0.593	201.2 Da LogP 0.19 TPSA 83.5	✓ Ro5	✓ Clean	`CC(=O)N[C@@H](C[C@H](C)C(C)=O)C(=O)O`
ZINC1602741	0.593	201.2 Da LogP 0.19 TPSA 83.5	✓ Ro5	✓ Clean	`CC(=O)N[C@@H](C[C@@H](C)C(C)=O)C(=O)O`
ZINC1602742	0.593	201.2 Da LogP 0.19 TPSA 83.5	✓ Ro5	✓ Clean	`CC(=O)N[C@H](C[C@H](C)C(C)=O)C(=O)O`
ZINC1602743	0.593	201.2 Da LogP 0.19 TPSA 83.5	✓ Ro5	✓ Clean	`CC(=O)N[C@H](C[C@@H](C)C(C)=O)C(=O)O`
ZINC4831627	0.593	370.5 Da LogP -0.21 TPSA 76.0	✓ Ro5	✓ Clean	`O=S(=O)(CC[n+]1ccccc1)CCS(=O)(=O)CC[n+]1ccccc1`
ZINC2560841	0.586	204.2 Da LogP -2.32 TPSA 115.7	✓ Ro5	✓ Clean	`CC(=O)N[C@@H](CO)C(=O)NCC(=O)O`
ZINC1706207	0.583	202.2 Da LogP 0.32 TPSA 69.7	✓ Ro5	✓ Clean	`CC(=O)OCC(COC(C)=O)C(C)=O`
ZINC100065511	0.576	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C(CO)[C@H](O)[C@H](O)[C@@H](O)COP(=O)(O)O`
ZINC100085043	0.576	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C(CO)[C@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC104869937	0.576	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C(CO)[C@H](O)[C@@H](O)[C@@H](O)COP(=O)(O)O`
ZINC13537943	0.576	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C(CO)[C@H](O)[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC85994845	0.576	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C(CO)[C@@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC2019971	0.571	205.2 Da LogP -0.14 TPSA 83.5	✓ Ro5	✓ Clean	`CC(=O)N[C@@H](CSC(C)=O)C(=O)O`
ZINC6186192	0.571	205.2 Da LogP -0.14 TPSA 83.5	✓ Ro5	✓ Clean	`CC(=O)N[C@H](CSC(C)=O)C(=O)O`
ZINC22112620	0.567	216.3 Da LogP 0.64 TPSA 58.3	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCC[n+]1ccccc1`
ZINC2539634	0.567	207.3 Da LogP -0.70 TPSA 86.6	✓ Ro5	✓ Clean	`CC(=O)N[C@@H](CSCCO)C(=O)O`
ZINC70665010	0.567	287.4 Da LogP 3.73 TPSA 72.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCOC[C@@H](N)C(=O)O`
ZINC71773060	0.567	207.2 Da LogP 0.37 TPSA 66.4	✓ Ro5	✓ Clean	`CC(=O)N[C@@H](CO)C(=O)c1ccccc1`
ZINC71773061	0.567	207.2 Da LogP 0.37 TPSA 66.4	✓ Ro5	✓ Clean	`CC(=O)N[C@H](CO)C(=O)c1ccccc1`
ZINC22067319	0.563	267.3 Da LogP -1.98 TPSA 127.1	✓ Ro5	✓ Clean	`CC(=O)N[C@@H](CSC[C@@H](O)[C@@H](O)CO)C(=O)O`
ZINC22067322	0.563	267.3 Da LogP -1.98 TPSA 127.1	✓ Ro5	✓ Clean	`CC(=O)N[C@@H](CSC[C@H](O)[C@@H](O)CO)C(=O)O`
ZINC22067325	0.563	267.3 Da LogP -1.98 TPSA 127.1	✓ Ro5	✓ Clean	`CC(=O)N[C@@H](CSC[C@@H](O)[C@H](O)CO)C(=O)O`
ZINC22067328	0.563	267.3 Da LogP -1.98 TPSA 127.1	✓ Ro5	✓ Clean	`CC(=O)N[C@@H](CSC[C@H](O)[C@H](O)CO)C(=O)O`
ZINC5132038	0.559	290.2 Da LogP -3.90 TPSA 185.0	1 viol.	✓ Clean	`O=C(CO)[C@@H](O)[C@H](O)[C@H](O)[C@H](O)COP(=O)…`
ZINC34182898	0.552	221.2 Da LogP -0.61 TPSA 103.7	✓ Ro5	✓ Clean	`CC(=O)N[C@H](CSCC(=O)O)C(=O)O`
ZINC34287799	0.552	213.2 Da LogP 0.92 TPSA 66.4	✓ Ro5	✓ Clean	`CC(=O)N[C@@H](CCC(F)(F)F)C(=O)O`
ZINC34287800	0.552	213.2 Da LogP 0.92 TPSA 66.4	✓ Ro5	✓ Clean	`CC(=O)N[C@H](CCC(F)(F)F)C(=O)O`
ZINC5167323	0.552	221.2 Da LogP -0.61 TPSA 103.7	✓ Ro5	✓ Clean	`CC(=O)N[C@@H](CSCC(=O)O)C(=O)O`

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.