Protein profile

PA4056

riboflavin-specific deaminase/reductase

Genome: NC_002516.2

Gene: PA4056 ribD Structure source: AlphaFold UniProt Q9HWX2

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Amino acids 373

Annotations 7

Features 24

PDB binders 12

Druggability 0.331

Overview

Basic information about this protein and its source genome.

Accession: PA4056
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA4056 ribD
Status: annotated
Amino acids: 373
Structure source: AlphaFold

GO:0008703 Catalysis of the reaction: 5-amino-6-(5-phosphoribitylamino)uracil + NADP+ = 5-amino-6-(5-phosphoribosylamino)uracil + H+ + NADPH. GO:0008835 Catalysis of the reaction: 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)-pyrimidine + H2O + H+ = 5-amino-6-(5-phosphoribosylamino)uracil + NH4. GO:0050661 Binding to nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH. GO:0008270 Binding to a zinc ion (Zn). GO:0009231 The chemical reactions and pathways resulting in the formation of riboflavin (vitamin B2), the precursor for the coenzymes flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD). GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Gut microbiome off-target: hit
Essential (DEG): Y
Localization: Cytoplasmic

Selected Druggability evidence

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 0.331

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

7 GO

Gene Ontology (GO)

GO:0008703 Catalysis of the reaction: 5-amino-6-(5-phosphoribitylamino)uracil + NADP+ = 5-amino-6-(5-phosphoribosylamino)uracil + H+ + NADPH.
GO:0008835 Catalysis of the reaction: 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)-pyrimidine + H2O + H+ = 5-amino-6-(5-phosphoribosylamino)uracil + NH4.
GO:0050661 Binding to nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
GO:0008270 Binding to a zinc ion (Zn).
GO:0009231 The chemical reactions and pathways resulting in the formation of riboflavin (vitamin B2), the precursor for the coenzymes flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD).
GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.

Sequence Features

Domain/signature hits from InterPro and related databases.

24 records

Show feature table

Start	End	DB	Term	Name
52	90	ProSitePatterns	PS00903	Cytidine and deoxycytidylate deaminases zinc-binding region signature.
52	90	InterPro	IPR016192	APOBEC/CMP deaminase, zinc-binding
148	367	NCBIfam	TIGR00227	riboflavin-specific deaminase C-terminal domain
148	367	InterPro	IPR011549	Riboflavin-specific deaminase, C-terminal
1	370	PIRSF	PIRSF006769	RibD
1	370	InterPro	IPR004794	Riboflavin biosynthesis protein RibD
149	363	Pfam	PF01872	RibD C-terminal domain
149	363	InterPro	IPR002734	Bacterial bifunctional deaminase-reductase, C-terminal
3	125	ProSiteProfiles	PS51747	Cytidine and deoxycytidylate deaminases domain profile.
3	125	InterPro	IPR002125	Cytidine and deoxycytidylate deaminase domain
9	121	CDD	cd01284	Riboflavin_deaminase-reductase
143	372	Gene3D	G3DSA:3.40.430.10	Dihydrofolate Reductase, subunit A
143	372	InterPro	IPR024072	Dihydrofolate reductase-like domain superfamily
9	364	NCBIfam	TIGR00326	bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase RibD
9	364	InterPro	IPR004794	Riboflavin biosynthesis protein RibD
147	365	SUPERFAMILY	SSF53597	Dihydrofolate reductase-like
147	365	InterPro	IPR024072	Dihydrofolate reductase-like domain superfamily
5	146	SUPERFAMILY	SSF53927	Cytidine deaminase-like
5	146	InterPro	IPR016193	Cytidine deaminase-like
2	142	FunFam	G3DSA:3.40.140.10:FF:000025	Riboflavin biosynthesis protein RibD
8	101	Pfam	PF00383	Cytidine and deoxycytidylate deaminase zinc-binding region
8	101	InterPro	IPR002125	Cytidine and deoxycytidylate deaminase domain
142	366	PANTHER	PTHR38011	DIHYDROFOLATE REDUCTASE FAMILY PROTEIN (AFU_ORTHOLOGUE AFUA_8G06820)
2	142	Gene3D	G3DSA:3.40.140.10	Cytidine Deaminase, domain 2

3D Structure

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

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Structural evidence

0 + 1

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

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold PA4056	AlphaFold	—	—	full sequence	—	Viewing

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
1				0.331
2				0.286

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.

62 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
44V	4XT6	P71968	181.2 Da LogP -0.42 TPSA 95.8	✓ Ro5	✓ Clean	`C[C@H]1CNC2=C(N1)C(=O)NC(=N2)N`
44W	4XT4	P71968	179.2 Da LogP -0.13 TPSA 96.2	✓ Ro5	✓ Clean	`CC1=NC2=C(NC1)N=C(NC2=O)N`
5GP	3ZPG	D0CB74	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O…`
AI9	4G3M	P17618	354.2 Da LogP -3.46 TPSA 231.5	1 viol.	✓ Clean	`C([C@H]([C@H]([C@H](/C=N/C1=C(C(=O)NC(=O)N1)N)O…`
AIF	3EX8	P17618	354.2 Da LogP -3.46 TPSA 231.5	1 viol.	✓ Clean	`C([C@H]([C@H]([C@@H](\C=N\C1=C(C(=O)NC(=O)N1)N)…`
AOF	4G3M	P17618	354.2 Da LogP -3.39 TPSA 220.2	1 viol.	✓ Clean	`C([C@@H]1[C@H]([C@H]([C@@H](O1)NC2=C(C(=O)NC(=O…`
CAC	3ZPG	D0CB74	137.0 Da LogP -0.52 TPSA 40.1	✓ Ro5	✓ Clean	`C[As](=O)(C)[O-]`
G8J	6DE5	P71968	373.5 Da LogP 3.43 TPSA 99.9	✓ Ro5	✓ Clean	`CCc1c(c(nc(n1)N)N)C#CC(C)c2cc(ccc2OC)c3ccncc3`
MA5	2AZN	Q58085	452.5 Da LogP -2.40 TPSA 178.5	2 viol.	✓ Clean	`C1CCC(CC1)CCO[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2…`
OXL	3ZPG	D0CB74	88.0 Da LogP -3.51 TPSA 80.3	✓ Ro5	✓ Clean	`C(=O)(C(=O)[O-])[O-]`
TMQ	4XT8	P71968	370.4 Da LogP 2.16 TPSA 118.8	✓ Ro5	Alert	`Cc1c(ccc2c1c(nc([nH+]2)N)N)CNc3cc(c(c(c3)OC)OC)…`
TOP	4XT7	P71968	290.3 Da LogP 1.26 TPSA 105.5	✓ Ro5	✓ Clean	`COc1cc(cc(c1OC)OC)Cc2cnc(nc2N)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).

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
ZINC12501413	1.000	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)…`
ZINC12958448	1.000	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@H](O)[…`
ZINC1532555	1.000	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[…`
ZINC16546189	1.000	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@H](O)[…`
ZINC2159505	1.000	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)…`
ZINC3073318	1.000	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)…`
ZINC3869963	1.000	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)…`
ZINC3869965	1.000	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@@H](COP(=O)(O)O)[C@@H](O…`
ZINC58649445	1.000	452.5 Da LogP -2.40 TPSA 178.5	2 viol.	✓ Clean	`OC[C@H]1O[C@H](O[C@@H]2[C@@H](CO)O[C@@H](OCCC3C…`
ZINC6627681	1.000	290.3 Da LogP 1.26 TPSA 105.5	✓ Ro5	✓ Clean	`COc1cc(Cc2cnc(N)nc2N)cc(OC)c1OC`
ZINC9334496	1.000	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[…`
ZINC104869865	0.857	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O…`
ZINC12504289	0.857	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC34541308	0.857	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC35000839	0.857	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC45284491	0.857	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC80639694	0.857	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC8215481	0.857	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC33494315	0.825	339.2 Da LogP 2.01 TPSA 96.3	✓ Ro5	✓ Clean	`COc1cc(Cc2cnc(N)nc2N)cc(Br)c1OC`
ZINC28006201	0.821	304.4 Da LogP 1.65 TPSA 105.5	✓ Ro5	✓ Clean	`CCOc1c(OC)cc(Cc2cnc(N)nc2N)cc1OC`
ZINC14881288	0.818	494.6 Da LogP -1.23 TPSA 178.5	2 viol.	✓ Clean	`OC[C@H]1O[C@H](O[C@@H]2[C@@H](CO)O[C@@H](OCCCCC…`
ZINC33979258	0.800	364.2 Da LogP -2.45 TPSA 200.2	1 viol.	✓ Clean	`O=c1[nH]c(O)nc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)…`
ZINC33979259	0.800	364.2 Da LogP -2.45 TPSA 200.2	1 viol.	✓ Clean	`O=c1[nH]c(O)nc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)…`
ZINC78920152	0.800	364.2 Da LogP -2.45 TPSA 200.2	1 viol.	✓ Clean	`O=c1[nH]c(O)nc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)…`
ZINC25725098	0.786	438.5 Da LogP -2.79 TPSA 178.5	2 viol.	✓ Clean	`OC[C@H]1O[C@H](O[C@@H]2[C@@H](CO)O[C@@H](OCC3CC…`
ZINC2020087	0.780	334.4 Da LogP 1.27 TPSA 114.7	✓ Ro5	✓ Clean	`COCCOc1c(OC)cc(Cc2cnc(N)nc2N)cc1OC`
ZINC28019914	0.780	319.4 Da LogP 0.59 TPSA 131.5	✓ Ro5	✓ Clean	`COc1cc(Cc2cnc(N)nc2N)cc(OC)c1OCCN`
ZINC13760474	0.769	276.3 Da LogP 0.95 TPSA 116.5	✓ Ro5	✓ Clean	`COc1cc(Cc2cnc(N)nc2N)cc(OC)c1O`
ZINC5824	0.769	339.2 Da LogP 2.01 TPSA 96.3	✓ Ro5	✓ Clean	`COc1cc(Cc2cnc(N)nc2N)cc(OC)c1Br`
ZINC28019236	0.762	333.4 Da LogP 0.98 TPSA 131.5	✓ Ro5	✓ Clean	`COc1cc(Cc2cnc(N)nc2N)cc(OC)c1OCCCN`
ZINC71774763	0.758	432.3 Da LogP -2.23 TPSA 198.3	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@](=O)(O)N3CCOCC3…`
ZINC12296728	0.741	347.2 Da LogP -1.54 TPSA 185.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@H]2C[C@@H](O)[C@@H](COP(=O)(O)O)…`
ZINC13527599	0.741	347.2 Da LogP -1.54 TPSA 185.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2C[C@@H](O)[C@@H](COP(=O)(O)O…`
ZINC13527603	0.741	347.2 Da LogP -1.54 TPSA 185.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2C[C@H](O)[C@@H](COP(=O)(O)O)…`
ZINC1532627	0.741	347.2 Da LogP -1.54 TPSA 185.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2C[C@@H](O)[C@H](COP(=O)(O)O)…`
ZINC1730395	0.741	347.2 Da LogP -1.54 TPSA 185.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@H]2C[C@H](O)[C@@H](COP(=O)(O)O)O…`
ZINC3869846	0.741	347.2 Da LogP -1.54 TPSA 185.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2C[C@H](O)[C@H](COP(=O)(O)O)O…`
ZINC3869847	0.741	347.2 Da LogP -1.54 TPSA 185.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@H]2C[C@H](O)[C@H](COP(=O)(O)O)O2…`
ZINC3869848	0.741	347.2 Da LogP -1.54 TPSA 185.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@H]2C[C@@H](O)[C@H](COP(=O)(O)O)O…`
ZINC4743771	0.741	361.3 Da LogP -2.70 TPSA 182.6	1 viol.	✓ Clean	`CS(=O)(=O)OC[C@H]1O[C@@H](n2cnc3c(=O)[nH]c(N)nc…`
ZINC4743772	0.741	361.3 Da LogP -2.70 TPSA 182.6	1 viol.	✓ Clean	`CS(=O)(=O)OC[C@@H]1O[C@@H](n2cnc3c(=O)[nH]c(N)n…`
ZINC4743774	0.741	361.3 Da LogP -2.70 TPSA 182.6	1 viol.	✓ Clean	`CS(=O)(=O)OC[C@H]1O[C@@H](n2cnc3c(=O)[nH]c(N)nc…`
ZINC4743775	0.741	361.3 Da LogP -2.70 TPSA 182.6	1 viol.	✓ Clean	`CS(=O)(=O)OC[C@@H]1O[C@@H](n2cnc3c(=O)[nH]c(N)n…`
ZINC14951284	0.732	348.2 Da LogP -2.15 TPSA 180.0	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C…`
ZINC1532551	0.732	348.2 Da LogP -2.15 TPSA 180.0	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@…`
ZINC16969369	0.732	348.2 Da LogP -2.15 TPSA 180.0	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@…`
ZINC4228242	0.732	348.2 Da LogP -2.15 TPSA 180.0	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@…`
ZINC4353761	0.732	348.2 Da LogP -2.15 TPSA 180.0	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C…`
ZINC8614392	0.732	348.2 Da LogP -2.15 TPSA 180.0	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C…`
ZINC1719	0.732	306.4 Da LogP 1.97 TPSA 96.3	✓ Ro5	✓ Clean	`COc1cc(Cc2cnc(N)nc2N)cc(OC)c1SC`

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.