Protein profile

KP13_02046

Riboflavin biosynthesis bifunctional protein ribD

Genome: KpKP13

Gene: AHE46049.1 ribD Structure source: AlphaFold + ColabFold UniProt A0A0H3GSM9

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Amino acids 367

Annotations 7

Features 25

PDB binders 7

Druggability 0.39

Overview

Basic information about this protein and its source genome.

Accession: KP13_02046
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE46049.1 ribD
Status: annotated
Amino acids: 367
Structure source: AlphaFold + ColabFold

GO:0008270 Binding to a zinc ion (Zn). 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:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. 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:0008703 Catalysis of the reaction: 5-amino-6-(5-phosphoribitylamino)uracil + NADP+ = 5-amino-6-(5-phosphoribosylamino)uracil + H+ + NADPH. 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.

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 (%): 86.921
DEG E-value: 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 96.74

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 0.39

Structure A0A0H3GSM9

Pocket Pocket 22

P2Rank 0.917

Structure A0A0H3GSM9

Pocket Pocket 1

ColabFold model

FPocket 0.822 · Pocket 26

P2Rank 0.92 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 172 / 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.

7 GO

Gene Ontology (GO)

GO:0008270 Binding to a zinc ion (Zn).
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:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
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:0008703 Catalysis of the reaction: 5-amino-6-(5-phosphoribitylamino)uracil + NADP+ = 5-amino-6-(5-phosphoribosylamino)uracil + H+ + NADPH.
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.
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.

Sequence Features

Domain/signature hits from InterPro and related databases.

25 records

Show feature table

Start	End	DB	Term	Name
144	362	SUPERFAMILY	SSF53597	Dihydrofolate reductase-like
144	362	InterPro	IPR024072	Dihydrofolate reductase-like domain superfamily
1	140	Gene3D	G3DSA:3.40.140.10	Cytidine Deaminase, domain 2
146	365	NCBIfam	TIGR00227	riboflavin-specific deaminase C-terminal domain
146	365	InterPro	IPR011549	Riboflavin-specific deaminase, C-terminal
50	88	ProSitePatterns	PS00903	Cytidine and deoxycytidylate deaminases zinc-binding region signature.
50	88	InterPro	IPR016192	APOBEC/CMP deaminase, zinc-binding
141	363	PANTHER	PTHR38011	DIHYDROFOLATE REDUCTASE FAMILY PROTEIN (AFU_ORTHOLOGUE AFUA_8G06820)
141	367	Gene3D	G3DSA:3.40.430.10	Dihydrofolate Reductase, subunit A
141	367	InterPro	IPR024072	Dihydrofolate reductase-like domain superfamily
141	366	FunFam	G3DSA:3.40.430.10:FF:000006	Riboflavin biosynthesis protein RibD
1	367	PIRSF	PIRSF006769	RibD
1	367	InterPro	IPR004794	Riboflavin biosynthesis protein RibD
147	362	Pfam	PF01872	RibD C-terminal domain
147	362	InterPro	IPR002734	Bacterial bifunctional deaminase-reductase, C-terminal
1	140	FunFam	G3DSA:3.40.140.10:FF:000025	Riboflavin biosynthesis protein RibD
7	362	NCBIfam	TIGR00326	bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase RibD
7	362	InterPro	IPR004794	Riboflavin biosynthesis protein RibD
2	99	Pfam	PF00383	Cytidine and deoxycytidylate deaminase zinc-binding region
2	99	InterPro	IPR002125	Cytidine and deoxycytidylate deaminase domain
3	145	SUPERFAMILY	SSF53927	Cytidine deaminase-like
3	145	InterPro	IPR016193	Cytidine deaminase-like
1	123	ProSiteProfiles	PS51747	Cytidine and deoxycytidylate deaminases domain profile.
1	123	InterPro	IPR002125	Cytidine and deoxycytidylate deaminase domain
7	119	CDD	cd01284	Riboflavin_deaminase-reductase

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_A0A0H3GSM9	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_02046	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
22				0.39

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	19.11	0.834
2	16.7	0.785
3	7.35	0.384
4	2.91	0.093
5	2.36	0.062

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
26				0.822
20				0.368
19				0.228

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	15.51	0.755
2	13.99	0.707
3	8.04	0.428
4	3.82	0.148
5	1.63	0.027

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.

57 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
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-]`
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-]`

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
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)[…`
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…`
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…`
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…`
ZINC1532637	0.722	283.2 Da LogP -2.69 TPSA 159.5	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO)[C@H](O)[C@@H]2O)c…`
ZINC1550030	0.722	283.2 Da LogP -2.69 TPSA 159.5	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)c…`
ZINC1570863	0.722	283.2 Da LogP -2.69 TPSA 159.5	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@H](CO)[C@@H](O)[C@H]2O)c(…`
ZINC1698205	0.722	283.2 Da LogP -2.69 TPSA 159.5	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@H](CO)[C@@H](O)[C@@H]2O)c…`
ZINC2020098	0.722	283.2 Da LogP -2.69 TPSA 159.5	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO)[C@H](O)[C@H]2O)c(…`
ZINC38580950	0.722	282.3 Da LogP -2.72 TPSA 165.3	✓ Ro5	✓ Clean	`NC[C@H]1O[C@@H](n2cnc3c(=O)[nH]c(N)nc32)[C@H](O…`
ZINC3869967	0.722	283.2 Da LogP -2.69 TPSA 159.5	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO)[C@@H](O)[C@H]2O)c…`
ZINC3869968	0.722	283.2 Da LogP -2.69 TPSA 159.5	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@@H](CO)[C@@H](O)[C@H]2O)…`
ZINC3869969	0.722	283.2 Da LogP -2.69 TPSA 159.5	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO)[C@@H](O)[C@@H]2O)…`
ZINC3869970	0.722	283.2 Da LogP -2.69 TPSA 159.5	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@@H](CO)[C@@H](O)[C@@H]2O…`
ZINC4990799	0.722	282.3 Da LogP -2.72 TPSA 165.3	✓ Ro5	✓ Clean	`NC[C@@H]1O[C@H](n2cnc3c(=O)[nH]c(N)nc32)[C@H](O…`
ZINC4990800	0.722	282.3 Da LogP -2.72 TPSA 165.3	✓ Ro5	✓ Clean	`NC[C@@H]1O[C@@H](n2cnc3c(=O)[nH]c(N)nc32)[C@H](…`
ZINC4990801	0.722	282.3 Da LogP -2.72 TPSA 165.3	✓ Ro5	✓ Clean	`NC[C@@H]1O[C@H](n2cnc3c(=O)[nH]c(N)nc32)[C@@H](…`
ZINC4990802	0.722	282.3 Da LogP -2.72 TPSA 165.3	✓ Ro5	✓ Clean	`NC[C@@H]1O[C@@H](n2cnc3c(=O)[nH]c(N)nc32)[C@@H]…`
ZINC5605239	0.722	283.2 Da LogP -2.69 TPSA 159.5	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@@H](CO)[C@H](O)[C@H]2O)c…`
ZINC6119283	0.722	283.2 Da LogP -2.69 TPSA 159.5	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO)[C@H](O)[C@H]2O)c(…`
ZINC6585367	0.722	283.2 Da LogP -2.69 TPSA 159.5	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO)[C@@H](O)[C@@H]2O)…`
ZINC8613125	0.722	283.2 Da LogP -2.69 TPSA 159.5	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO)[C@H](O)[C@@H]2O)c…`
ZINC97973759	0.722	282.3 Da LogP -2.72 TPSA 165.3	✓ Ro5	✓ Clean	`NC[C@H]1O[C@@H](n2cnc3c(=O)[nH]c(N)nc32)[C@H](O…`
ZINC97973760	0.722	282.3 Da LogP -2.72 TPSA 165.3	✓ Ro5	✓ Clean	`NC[C@H]1O[C@@H](n2cnc3c(=O)[nH]c(N)nc32)[C@@H](…`
ZINC12501360	0.689	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO)[C@@H](O)[C@@H]2OP…`
ZINC100727895	0.678	347.2 Da LogP -2.50 TPSA 196.8	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO)[C@@H](O)[C@H]2P(=…`
ZINC17610743	0.678	347.2 Da LogP -2.50 TPSA 196.8	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO)[C@@H](O)[C@@H]2P(…`
ZINC38580951	0.678	308.3 Da LogP -1.37 TPSA 188.0	✓ Ro5	Alert	`[N-]=[N+]=NC[C@H]1O[C@@H](n2cnc3c(=O)[nH]c(N)nc…`
ZINC5030599	0.678	308.3 Da LogP -1.37 TPSA 188.0	✓ Ro5	Alert	`[N-]=[N+]=NC[C@@H]1O[C@H](n2cnc3c(=O)[nH]c(N)nc…`
ZINC5030600	0.678	308.3 Da LogP -1.37 TPSA 188.0	✓ Ro5	Alert	`[N-]=[N+]=NC[C@@H]1O[C@@H](n2cnc3c(=O)[nH]c(N)n…`
ZINC5030605	0.678	308.3 Da LogP -1.37 TPSA 188.0	✓ Ro5	Alert	`[N-]=[N+]=NC[C@@H]1O[C@H](n2cnc3c(=O)[nH]c(N)nc…`
ZINC5030606	0.678	308.3 Da LogP -1.37 TPSA 188.0	✓ Ro5	Alert	`[N-]=[N+]=NC[C@@H]1O[C@@H](n2cnc3c(=O)[nH]c(N)n…`
ZINC38308095	0.651	384.4 Da LogP -3.96 TPSA 178.5	2 viol.	✓ Clean	`CCCO[C@@H]1O[C@H](CO)[C@@H](O[C@@H]2O[C@H](CO)[…`
ZINC17420659	0.650	297.3 Da LogP -2.03 TPSA 148.5	✓ Ro5	✓ Clean	`CO[C@H]1[C@@H](CO)O[C@@H](n2cnc3c(=O)[nH]c(N)nc…`
ZINC2522481	0.650	297.3 Da LogP -2.03 TPSA 148.5	✓ Ro5	✓ Clean	`CO[C@H]1[C@H](CO)O[C@H](n2cnc3c(=O)[nH]c(N)nc32…`
ZINC4963099	0.650	297.3 Da LogP -2.03 TPSA 148.5	✓ Ro5	✓ Clean	`CO[C@@H]1[C@H](CO)O[C@H](n2cnc3c(=O)[nH]c(N)nc3…`
ZINC4963101	0.650	297.3 Da LogP -2.03 TPSA 148.5	✓ Ro5	✓ Clean	`CO[C@H]1[C@H](CO)O[C@H](n2cnc3c(=O)[nH]c(N)nc32…`
ZINC4963103	0.650	297.3 Da LogP -2.03 TPSA 148.5	✓ Ro5	✓ Clean	`CO[C@@H]1[C@@H](CO)O[C@H](n2cnc3c(=O)[nH]c(N)nc…`
ZINC4963104	0.650	297.3 Da LogP -2.03 TPSA 148.5	✓ Ro5	✓ Clean	`CO[C@H]1[C@@H](CO)O[C@H](n2cnc3c(=O)[nH]c(N)nc3…`
ZINC5998227	0.650	297.3 Da LogP -2.03 TPSA 148.5	✓ Ro5	✓ Clean	`CO[C@@H]1[C@@H](CO)O[C@@H](n2cnc3c(=O)[nH]c(N)n…`
ZINC82188588	0.650	297.3 Da LogP -2.03 TPSA 148.5	✓ Ro5	✓ Clean	`CO[C@H]1[C@H](O)[C@H](n2cnc3c(=O)[nH]c(N)nc32)O…`
ZINC82188589	0.650	297.3 Da LogP -2.03 TPSA 148.5	✓ Ro5	✓ Clean	`CO[C@@H]1[C@H](O)[C@H](n2cnc3c(=O)[nH]c(N)nc32)…`
ZINC83290877	0.650	297.3 Da LogP -2.03 TPSA 148.5	✓ Ro5	✓ Clean	`CO[C@@H]1[C@H](CO)O[C@H](n2cnc3c(=O)[nH]c(N)nc3…`
ZINC4743778	0.636	437.4 Da LogP -0.97 TPSA 182.6	1 viol.	✓ Clean	`Cc1ccc(S(=O)(=O)OC[C@H]2O[C@@H](n3cnc4c(=O)[nH]…`
ZINC4743780	0.636	437.4 Da LogP -0.97 TPSA 182.6	1 viol.	✓ Clean	`Cc1ccc(S(=O)(=O)OC[C@@H]2O[C@@H](n3cnc4c(=O)[nH…`
ZINC4743782	0.636	437.4 Da LogP -0.97 TPSA 182.6	1 viol.	✓ Clean	`Cc1ccc(S(=O)(=O)OC[C@H]2O[C@@H](n3cnc4c(=O)[nH]…`
ZINC4743783	0.636	437.4 Da LogP -0.97 TPSA 182.6	1 viol.	✓ Clean	`Cc1ccc(S(=O)(=O)OC[C@@H]2O[C@@H](n3cnc4c(=O)[nH…`
ZINC6585366	0.627	285.2 Da LogP -1.71 TPSA 139.3	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO)[C@@H](F)[C@@H]2O)…`
ZINC78175055	0.627	282.3 Da LogP -2.72 TPSA 165.3	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO)[C@@H](O)[C@H]2N)c…`
ZINC78175062	0.627	282.3 Da LogP -2.72 TPSA 165.3	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO)[C@H](O)[C@@H]2N)c…`

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.