Protein profile

KP13_00723

cAMP receptor protein

Genome: KpKP13

Gene: crp AHE42341.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GYD6

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Amino acids 210

Annotations 8

Features 36

PDB binders 8

Druggability 0.91

Overview

Basic information about this protein and its source genome.

Accession: KP13_00723
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: crp AHE42341.1
Status: annotated
Amino acids: 210
Structure source: AlphaFold + ColabFold

GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). 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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0032993 A macromolecular complex containing both protein and DNA molecules. GO:0030552 Binding to cAMP, the nucleotide cyclic AMP (adenosine 3',5'-cyclophosphate).

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 30.682
Human E-value: 6.97e-06
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 94.48

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 0.91

Structure A0A0H3GYD6

Pocket Pocket 13

P2Rank 0.554

Structure A0A0H3GYD6

Pocket Pocket 1

ColabFold model

FPocket 0.717 · Pocket 7

P2Rank 0.498 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 170 / 4744 genomes with a hit

Normalized 0.036

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

8 GO

Gene Ontology (GO)

GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0032993 A macromolecular complex containing both protein and DNA molecules.
GO:0030552 Binding to cAMP, the nucleotide cyclic AMP (adenosine 3',5'-cyclophosphate).
GO:0043565 Binding to DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
GO:0045893 Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.

Sequence Features

Domain/signature hits from InterPro and related databases.

36 records

Show feature table

Start	End	DB	Term	Name
30	46	ProSitePatterns	PS00888	Cyclic nucleotide-binding domain signature 1.
30	46	InterPro	IPR018488	Cyclic nucleotide-binding, conserved site
142	206	Pfam	PF13545	Crp-like helix-turn-helix domain
142	206	InterPro	IPR012318	Crp-type HTH domain
1	132	Gene3D	G3DSA:2.60.120.10	Jelly Rolls
1	132	InterPro	IPR014710	RmlC-like jelly roll fold
160	208	SMART	SM00419	crpmeuga4
160	208	InterPro	IPR012318	Crp-type HTH domain
71	89	ProSitePatterns	PS00889	Cyclic nucleotide-binding domain signature 2.
71	89	InterPro	IPR018488	Cyclic nucleotide-binding, conserved site
1	132	FunFam	G3DSA:2.60.120.10:FF:000001	cAMP-activated global transcriptional regulator CRP
8	136	SUPERFAMILY	SSF51206	cAMP-binding domain-like
8	136	InterPro	IPR018490	Cyclic nucleotide-binding domain superfamily
140	207	CDD	cd00092	HTH_CRP
2	122	SMART	SM00100	cnmp_10
2	122	InterPro	IPR000595	Cyclic nucleotide-binding domain
139	207	SUPERFAMILY	SSF46785	Winged helix DNA-binding domain
139	207	InterPro	IPR036390	Winged helix DNA-binding domain superfamily
24	124	ProSiteProfiles	PS50042	cAMP/cGMP binding motif profile.
24	124	InterPro	IPR000595	Cyclic nucleotide-binding domain
166	182	PRINTS	PR00034	CRP bacterial regulatory protein HTH signature
166	182	InterPro	IPR012318	Crp-type HTH domain
182	197	PRINTS	PR00034	CRP bacterial regulatory protein HTH signature
182	197	InterPro	IPR012318	Crp-type HTH domain
138	210	ProSiteProfiles	PS51063	Crp-type HTH domain profile.
138	210	InterPro	IPR012318	Crp-type HTH domain
139	207	FunFam	G3DSA:1.10.10.10:FF:000006	cAMP-activated global transcriptional regulator CRP
139	207	Gene3D	G3DSA:1.10.10.10	-
139	207	InterPro	IPR036388	Winged helix-like DNA-binding domain superfamily
8	201	PANTHER	PTHR24567	CRP FAMILY TRANSCRIPTIONAL REGULATORY PROTEIN
168	191	ProSitePatterns	PS00042	Crp-type HTH domain signature.
168	191	InterPro	IPR018335	Transcription regulator HTH, Crp-type, conserved site
8	117	CDD	cd00038	CAP_ED
8	117	InterPro	IPR000595	Cyclic nucleotide-binding domain
23	109	Pfam	PF00027	Cyclic nucleotide-binding domain
23	109	InterPro	IPR000595	Cyclic nucleotide-binding domain

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_A0A0H3GYD6	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_00723	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
13				0.91

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				5.72	0.277
2				4.87	0.218

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
7				0.717

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				5.42	0.258
2				3.73	0.143

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
2FT	3LA3	P0A4U6	168.1 Da LogP 0.57 TPSA 74.6	✓ Ro5	✓ Clean	`C(CC(C(=O)O)(F)F)C(=O)O`
3C4	3E5U	B8FW11	186.6 Da LogP 1.67 TPSA 57.5	✓ Ro5	✓ Clean	`c1cc(c(cc1CC(=O)O)Cl)O`
AKG	3LA2	P0A4U6	146.1 Da LogP -0.50 TPSA 91.7	✓ Ro5	✓ Clean	`C(CC(=O)O)C(=O)C(=O)O`
BTB	2XGX	P29283	209.2 Da LogP -3.01 TPSA 104.4	✓ Ro5	✓ Clean	`C(CO)N(CCO)C(CO)(CO)CO`
N6R	3I59	P9WMH3	447.4 Da LogP 1.64 TPSA 140.8	✓ Ro5	✓ Clean	`C[C@H](Cc1ccccc1)Nc2c3c(ncn2)n(cn3)[C@H]4[C@@H]…`
N6S	3I59	P9WMH3	447.4 Da LogP 1.64 TPSA 140.8	✓ Ro5	✓ Clean	`C[C@@H](Cc1ccccc1)Nc2c3c(ncn2)n(cn3)[C@H]4[C@@H…`
PCG	4N9I	C3SQJ7	345.2 Da LogP -1.52 TPSA 174.8	✓ Ro5	✓ Clean	`c1nc2c(n1[C@H]3[C@@H]([C@H]4C(O3)CO[P@](=O)(O4)…`
SP1	4R8H	P0ACJ8	345.3 Da LogP -0.70 TPSA 137.8	✓ Ro5	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@H]4[C@H](O3)C…`

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
ZINC1615342	1.000	209.2 Da LogP -3.01 TPSA 104.4	✓ Ro5	✓ Clean	`OCCN(CCO)C(CO)(CO)CO`
ZINC12502230	0.782	329.2 Da LogP -0.82 TPSA 154.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H]2CO[P@](=O)(O)O[C@@…`
ZINC3581269	0.782	329.2 Da LogP -0.82 TPSA 154.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H]2CO[P@](=O)(O)O[C@H…`
ZINC3869448	0.782	329.2 Da LogP -0.82 TPSA 154.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H]2CO[P@](=O)(O)O[C@@H]…`
ZINC3869449	0.782	329.2 Da LogP -0.82 TPSA 154.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H]2CO[P@](=O)(O)O[C@@H…`
ZINC3869450	0.782	329.2 Da LogP -0.82 TPSA 154.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H]2CO[P@](=O)(O)O[C@@H]…`
ZINC3869451	0.782	329.2 Da LogP -0.82 TPSA 154.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H]2CO[P@](=O)(O)O[C@@H…`
ZINC3873977	0.782	329.2 Da LogP -0.82 TPSA 154.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H]2CO[P@](=O)(O)O[C@H…`
ZINC4245698	0.782	329.2 Da LogP -0.82 TPSA 154.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H]2CO[P@](=O)(O)O[C@@…`
ZINC156509	0.714	205.0 Da LogP 2.62 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)Cc1ccc(Cl)c(Cl)c1`
ZINC43476834	0.677	200.6 Da LogP 2.06 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)CCc1ccc(O)c(Cl)c1`
ZINC1857721041	0.676	262.7 Da LogP 3.34 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)Cc1cccc(-c2ccc(O)c(Cl)c2)c1`
ZINC5158647	0.667	357.3 Da LogP 0.23 TPSA 143.8	1 viol.	✓ Clean	`CCO[P@@]1(=O)OC[C@H]2O[C@@H](n3cnc4c(N)ncnc43)[…`
ZINC5158648	0.667	357.3 Da LogP 0.23 TPSA 143.8	1 viol.	✓ Clean	`CCO[P@]1(=O)OC[C@H]2O[C@@H](n3cnc4c(N)ncnc43)[C…`
ZINC5158649	0.667	357.3 Da LogP 0.23 TPSA 143.8	1 viol.	✓ Clean	`CCO[P@@]1(=O)OC[C@@H]2O[C@@H](n3cnc4c(N)ncnc43)…`
ZINC5158650	0.667	357.3 Da LogP 0.23 TPSA 143.8	1 viol.	✓ Clean	`CCO[P@]1(=O)OC[C@@H]2O[C@@H](n3cnc4c(N)ncnc43)[…`
ZINC78710634	0.645	249.5 Da LogP 2.73 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)Cc1ccc(Br)c(Cl)c1`
ZINC38580930	0.636	401.3 Da LogP -0.27 TPSA 170.1	1 viol.	✓ Clean	`CC(=O)OCO[P@@]1(=O)OC[C@H]2O[C@@H](n3cnc4c(N)nc…`
ZINC38627784	0.636	401.3 Da LogP -0.27 TPSA 170.1	1 viol.	✓ Clean	`CC(=O)OCO[P@]1(=O)OC[C@H]2O[C@@H](n3cnc4c(N)ncn…`
ZINC5997107	0.636	200.6 Da LogP 1.76 TPSA 46.5	✓ Ro5	✓ Clean	`COC(=O)Cc1ccc(O)c(Cl)c1`
ZINC4822013	0.617	307.3 Da LogP -0.18 TPSA 117.5	✓ Ro5	✓ Clean	`CC1(C)OC[C@H]2O[C@@H](n3cnc4c(N)ncnc43)[C@@H](O…`
ZINC4822015	0.617	307.3 Da LogP -0.18 TPSA 117.5	✓ Ro5	✓ Clean	`CC1(C)OC[C@@H]2O[C@@H](n3cnc4c(N)ncnc43)[C@@H](…`
ZINC4822016	0.617	307.3 Da LogP -0.18 TPSA 117.5	✓ Ro5	✓ Clean	`CC1(C)OC[C@H]2O[C@@H](n3cnc4c(N)ncnc43)[C@@H](O…`
ZINC4822019	0.617	307.3 Da LogP -0.18 TPSA 117.5	✓ Ro5	✓ Clean	`CC1(C)OC[C@@H]2O[C@@H](n3cnc4c(N)ncnc43)[C@@H](…`
ZINC142788982	0.613	202.6 Da LogP 1.38 TPSA 77.8	✓ Ro5	Alert	`O=C(O)Cc1cc(O)c(O)c(Cl)c1`
ZINC2566063	0.613	231.0 Da LogP 1.78 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)Cc1ccc(O)c(Br)c1`
ZINC96334879	0.613	278.0 Da LogP 1.62 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)Cc1ccc(O)c(I)c1`
ZINC575442361	0.606	212.6 Da LogP 2.17 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)c1ccc(CC(=O)O)cc1Cl`
ZINC139845874	0.594	296.5 Da LogP 2.57 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)Cc1ccc(Cl)c(I)c1`
ZINC71792958	0.594	249.5 Da LogP 2.73 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)Cc1ccc(Cl)c(Br)c1`
ZINC2530927	0.591	242.1 Da LogP 2.68 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)CCC(F)(C(F)(F)F)C(F)(F)F`
ZINC2530939	0.591	292.1 Da LogP 3.52 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)CCC(C(F)(F)F)(C(F)(F)F)C(F)(F)F`
ZINC2555157	0.591	203.0 Da LogP 1.84 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)CCC(F)(F)Br`
ZINC2507572	0.588	215.6 Da LogP 1.88 TPSA 80.4	✓ Ro5	✓ Clean	`O=C(O)Cc1ccc([N+](=O)[O-])c(Cl)c1`
ZINC3750728	0.588	200.6 Da LogP 1.98 TPSA 46.5	✓ Ro5	✓ Clean	`COc1ccc(CC(=O)O)cc1Cl`
ZINC37594129	0.588	216.7 Da LogP 2.69 TPSA 37.3	✓ Ro5	✓ Clean	`CSc1ccc(CC(=O)O)cc1Cl`
ZINC44375842	0.588	238.6 Da LogP 2.99 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)Cc1ccc(C(F)(F)F)c(Cl)c1`
ZINC76164133	0.588	216.6 Da LogP 1.03 TPSA 77.8	✓ Ro5	✓ Clean	`O=C(O)[C@@H](O)Cc1ccc(O)c(Cl)c1`
ZINC76164134	0.588	216.6 Da LogP 1.03 TPSA 77.8	✓ Ro5	✓ Clean	`O=C(O)[C@H](O)Cc1ccc(O)c(Cl)c1`
ZINC601703663	0.583	228.7 Da LogP 2.54 TPSA 46.5	✓ Ro5	✓ Clean	`CC(C)OC(=O)Cc1ccc(O)c(Cl)c1`
ZINC909996795	0.583	237.7 Da LogP 1.99 TPSA 40.5	✓ Ro5	✓ Clean	`O=C(Cc1ccc(O)c(Cl)c1)N1CC=CC1`
ZINC1712438	0.571	248.2 Da LogP -0.13 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)CCC(CCC(=O)O)(C(=O)O)C(=O)O`
ZINC402813	0.571	215.6 Da LogP 1.00 TPSA 83.5	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(O)c(Cl)c1)C(=O)O`
ZINC402814	0.571	215.6 Da LogP 1.00 TPSA 83.5	✓ Ro5	✓ Clean	`N[C@H](Cc1ccc(O)c(Cl)c1)C(=O)O`
ZINC97758156	0.571	248.7 Da LogP 1.37 TPSA 71.4	✓ Ro5	✓ Clean	`CS(=O)(=O)c1ccc(CC(=O)O)cc1Cl`
ZINC5139067	0.564	283.3 Da LogP -1.04 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CS)[C@@H](O)[C@H]1O`
ZINC1758568	0.563	218.7 Da LogP 3.64 TPSA 20.2	✓ Ro5	✓ Clean	`Oc1ccc(Cc2ccccc2)cc1Cl`
ZINC38580931	0.563	345.2 Da LogP -1.58 TPSA 168.9	✓ Ro5	✓ Clean	`Nc1c2ncn([C@@H]3O[C@@H]4CO[P@](=O)(O)O[C@H]4[C@…`
ZINC83072638	0.563	231.0 Da LogP 1.78 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)Cc1ccc(Br)c(O)c1`
ZINC220561339	0.561	313.8 Da LogP 2.59 TPSA 86.6	✓ Ro5	✓ Clean	`CC(C)C[C@H](CC(=O)O)NC(=O)Cc1ccc(O)c(Cl)c1`

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.