Protein profile

KP13_00998

hypothetical protein

Genome: KpKP13

Gene: AHE43472.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GVR0

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Amino acids 199

Annotations 5

Features 14

PDB binders 5

Druggability 0.233

Overview

Basic information about this protein and its source genome.

Accession: KP13_00998
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE43472.1
Status: annotated
Amino acids: 199
Structure source: AlphaFold + ColabFold

3.1.3.89

GO:0002953 Catalysis of the reaction: a 2'-deoxyribonucleoside 5'-phosphate + H2O = a 2'-deoxyribonucleoside + phosphate. GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0046872 Binding to a metal ion. GO:0000166 Binding to a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 95.7

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 0.233

Structure A0A0H3GVR0

Pocket Pocket 3

P2Rank 0.953

Structure A0A0H3GVR0

Pocket Pocket 1

ColabFold model

FPocket 0.141 · Pocket 5

P2Rank 0.952 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 234 / 4744 genomes with a hit

Normalized 0.049

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

3.1.3.89

Gene Ontology (GO)

GO:0002953 Catalysis of the reaction: a 2'-deoxyribonucleoside 5'-phosphate + H2O = a 2'-deoxyribonucleoside + phosphate.
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0046872 Binding to a metal ion.
GO:0000166 Binding to a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.

Sequence Features

Domain/signature hits from InterPro and related databases.

14 records

Show feature table

Start	End	DB	Term	Name
26	151	SMART	SM00471	hd_13
26	151	InterPro	IPR003607	HD/PDEase domain
3	195	Hamap	MF_01100	5'-deoxynucleotidase YfbR [yfbR].
3	195	InterPro	IPR022971	5'-deoxynucleotidase YfbR
5	186	Pfam	PF12917	5'-deoxynucleotidase YfbR-like
3	185	SUPERFAMILY	SSF109604	HD-domain/PDEase-like
1	199	Gene3D	G3DSA:1.10.3210.10	Hypothetical protein af1432
28	124	CDD	cd00077	HDc
28	124	InterPro	IPR003607	HD/PDEase domain
5	154	PANTHER	PTHR11845	UNCHARACTERIZED
5	154	InterPro	IPR039356	5'-deoxynucleotidase YfbR/HDDC2
30	142	ProSiteProfiles	PS51831	HD domain profile.
30	142	InterPro	IPR006674	HD domain
1	199	FunFam	G3DSA:1.10.3210.10:FF:000002	Nucleotidase YfbR

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_A0A0H3GVR0	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_00998	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
3				0.233

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	30.27	0.934
2	1.88	0.037
3	1.34	0.015

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				29.08	0.929
2				2.27	0.057

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.

55 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
7D3	5TK6	O24769	411.2 Da LogP -0.86 TPSA 212.4	1 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@H](O3)COP(=O)…`
7D4	5TK7	O24769	491.2 Da LogP -0.74 TPSA 258.9	2 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@H](O3)COP(=O)…`
7D5	5TK8	O24769	331.2 Da LogP -0.98 TPSA 165.8	✓ Ro5	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@H](O3)COP(=O)…`
7D7	5TK9	O24769	251.2 Da LogP -1.09 TPSA 119.3	✓ Ro5	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@H](O3)CO)CO)N`
D5M	2PAU	P76491	331.2 Da LogP -0.83 TPSA 165.8	✓ Ro5	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)COP(=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
ZINC12958401	1.000	331.2 Da LogP -0.83 TPSA 165.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1C[C@@H](O)[C@@H](COP(=O)(O)…`
ZINC13538980	1.000	331.2 Da LogP -0.83 TPSA 165.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1C[C@@H](O)[C@@H](COP(=O)(O…`
ZINC13538982	1.000	331.2 Da LogP -0.83 TPSA 165.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1C[C@H](O)[C@@H](COP(=O)(O)…`
ZINC1532626	1.000	331.2 Da LogP -0.83 TPSA 165.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1C[C@@H](O)[C@H](COP(=O)(O)…`
ZINC1713574	1.000	331.2 Da LogP -0.83 TPSA 165.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1C[C@H](O)[C@@H](COP(=O)(O)O…`
ZINC3869813	1.000	331.2 Da LogP -0.83 TPSA 165.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1C[C@H](O)[C@H](COP(=O)(O)O…`
ZINC3869814	1.000	331.2 Da LogP -0.83 TPSA 165.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1C[C@H](O)[C@H](COP(=O)(O)O)…`
ZINC3869815	1.000	331.2 Da LogP -0.83 TPSA 165.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1C[C@@H](O)[C@H](COP(=O)(O)O…`
ZINC12495199	0.849	411.2 Da LogP -0.72 TPSA 212.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1C[C@H](O)[C@@H](CO[P@@](=O…`
ZINC13434873	0.849	411.2 Da LogP -0.72 TPSA 212.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1C[C@H](O)[C@H](CO[P@@](=O)…`
ZINC13434875	0.849	411.2 Da LogP -0.72 TPSA 212.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1C[C@H](O)[C@H](CO[P@@](=O)(…`
ZINC13434876	0.849	411.2 Da LogP -0.72 TPSA 212.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1C[C@@H](O)[C@H](CO[P@](=O)…`
ZINC13434878	0.849	411.2 Da LogP -0.72 TPSA 212.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1C[C@@H](O)[C@H](CO[P@@](=O)…`
ZINC8215728	0.849	411.2 Da LogP -0.72 TPSA 212.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1C[C@H](O)[C@@H](CO[P@@](=O)…`
ZINC13434879	0.833	491.2 Da LogP -0.60 TPSA 258.9	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1C[C@H](O)[C@H](CO[P@@](=O)…`
ZINC13434881	0.833	491.2 Da LogP -0.60 TPSA 258.9	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1C[C@H](O)[C@H](CO[P@@](=O)(…`
ZINC13434883	0.833	491.2 Da LogP -0.60 TPSA 258.9	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1C[C@@H](O)[C@H](CO[P@@](=O…`
ZINC13434884	0.833	491.2 Da LogP -0.60 TPSA 258.9	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1C[C@@H](O)[C@H](CO[P@@](=O)…`
ZINC8215662	0.833	491.2 Da LogP -0.60 TPSA 258.9	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1C[C@H](O)[C@@H](CO[P@@](=O)…`
ZINC8664605	0.833	491.2 Da LogP -0.60 TPSA 258.9	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1C[C@H](O)[C@@H](CO[P@@](=O…`
ZINC13522804	0.788	332.2 Da LogP -0.71 TPSA 160.1	✓ Ro5	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@@H](n2cnc3c(O)ncnc32)C[C@@…`
ZINC13518964	0.722	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC1532515	0.722	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@H](O…`
ZINC1571045	0.722	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC1842158	0.722	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@H](O…`
ZINC2046931	0.722	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC2126310	0.722	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3201891	0.722	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC3201893	0.722	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3830180	0.722	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3860156	0.722	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3977897	0.722	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](COP(=O)(O)O)[C@@H](O…`
ZINC4806442	0.722	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC8613167	0.722	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC12501123	0.714	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC4228234	0.714	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC79671662	0.714	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC79671663	0.714	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC1081581	0.706	251.2 Da LogP -0.95 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1C[C@H](O)[C@@H](CO)O1`
ZINC15958242	0.706	251.2 Da LogP -0.95 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1C[C@H](O)[C@H](CO)O1`
ZINC1842582	0.706	251.2 Da LogP -0.95 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1C[C@H](O)[C@H](CO)O1`
ZINC3581934	0.706	250.3 Da LogP -0.98 TPSA 125.1	✓ Ro5	✓ Clean	`NC[C@@H]1O[C@H](n2cnc3c(N)ncnc32)C[C@@H]1O`
ZINC3590982	0.706	250.3 Da LogP -0.98 TPSA 125.1	✓ Ro5	✓ Clean	`NC[C@@H]1O[C@H](n2cnc3c(N)ncnc32)C[C@H]1O`
ZINC3869836	0.706	251.2 Da LogP -0.95 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1C[C@@H](O)[C@H](CO)O1`
ZINC39105	0.706	251.2 Da LogP -0.95 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1C[C@@H](O)[C@H](CO)O1`
ZINC3978745	0.706	251.2 Da LogP -0.95 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1C[C@H](O)[C@@H](CO)O1`
ZINC4822618	0.706	250.3 Da LogP -0.98 TPSA 125.1	✓ Ro5	✓ Clean	`NC[C@@H]1O[C@@H](n2cnc3c(N)ncnc32)C[C@@H]1O`
ZINC4822620	0.706	250.3 Da LogP -0.98 TPSA 125.1	✓ Ro5	✓ Clean	`NC[C@@H]1O[C@@H](n2cnc3c(N)ncnc32)C[C@H]1O`
ZINC9214234	0.706	251.2 Da LogP -0.95 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1C[C@@H](O)[C@@H](CO)O1`
ZINC9214236	0.706	251.2 Da LogP -0.95 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1C[C@@H](O)[C@@H](CO)O1`

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.