Protein profile

KP13_01850

2'-5'-RNA ligase

Genome: KpKP13

Gene: ligT AHE46290.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GNF0

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Amino acids 178

Annotations 4

Features 13

PDB binders 1

Druggability 0.258

Overview

Basic information about this protein and its source genome.

Accession: KP13_01850
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: ligT AHE46290.1
Status: annotated
Amino acids: 178
Structure source: AlphaFold + ColabFold

3.1.4.58

GO:0008664 Catalysis the reaction: a 3'-end 2',3'-cyclophospho-ribonucleotide-RNA + H2O = a 3'-end 2'-phospho-ribonucleotide-RNA + H+. GO:0004113 Catalysis of the reaction: nucleoside 2',3'-cyclic phosphate + H2O = nucleoside 2'-phosphate. GO:0016874 Catalysis of the joining of two molecules, or two groups within a single molecule, using the energy from the hydrolysis of ATP, a similar triphosphate, or a pH gradient.

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: Unknown
ColabFold pLDDT: 94.44

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 0.258

Structure A0A0H3GNF0

Pocket Pocket 9

P2Rank 0.721

Structure A0A0H3GNF0

Pocket Pocket 1

ColabFold model

FPocket 0.364 · Pocket 4

P2Rank 0.827 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 92 / 4744 genomes with a hit

Normalized 0.019

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 3 GO

Enzyme Commission (EC)

3.1.4.58

Gene Ontology (GO)

GO:0008664 Catalysis the reaction: a 3'-end 2',3'-cyclophospho-ribonucleotide-RNA + H2O = a 3'-end 2'-phospho-ribonucleotide-RNA + H+.
GO:0004113 Catalysis of the reaction: nucleoside 2',3'-cyclic phosphate + H2O = nucleoside 2'-phosphate.
GO:0016874 Catalysis of the joining of two molecules, or two groups within a single molecule, using the energy from the hydrolysis of ATP, a similar triphosphate, or a pH gradient.

Sequence Features

Domain/signature hits from InterPro and related databases.

13 records

Show feature table

Start	End	DB	Term	Name
5	174	Hamap	MF_01940	RNA 2',3'-cyclic phosphodiesterase [thpR].
5	174	InterPro	IPR004175	RNA 2',3'-cyclic phosphodiesterase
5	175	SUPERFAMILY	SSF55144	LigT-like
5	175	InterPro	IPR009097	Cyclic phosphodiesterase
11	89	Pfam	PF02834	LigT like Phosphoesterase
11	89	InterPro	IPR014051	Phosphoesterase, HXTX
92	166	Pfam	PF02834	LigT like Phosphoesterase
92	166	InterPro	IPR014051	Phosphoesterase, HXTX
1	174	Gene3D	G3DSA:3.90.1140.10	Cyclic phosphodiesterase
6	173	NCBIfam	TIGR02258	RNA 2',3'-cyclic phosphodiesterase
6	173	InterPro	IPR004175	RNA 2',3'-cyclic phosphodiesterase
2	175	PANTHER	PTHR35561	RNA 2',3'-CYCLIC PHOSPHODIESTERASE
2	175	InterPro	IPR004175	RNA 2',3'-cyclic phosphodiesterase

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_A0A0H3GNF0	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_01850	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
9				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	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				10.41	0.56

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				0.364

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				14.76	0.734

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.

51 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
2AM	4QAK	P37025	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`

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
ZINC13424932	1.000	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O)[C@@H]1…`
ZINC13424933	1.000	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO)[C@@H](O)[C@@H]1O…`
ZINC2036187	1.000	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](O)[C@H]1OP…`
ZINC3861741	1.000	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O…`
ZINC44960119	1.000	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](O)[C@@H]1O…`
ZINC4513863	1.000	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@@H]1…`
ZINC4513866	1.000	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@@H]…`
ZINC12958381	0.882	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](OP(=O)(O)…`
ZINC13546985	0.882	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](OP(=O)(O)O…`
ZINC1631259	0.882	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](OP(=O)(O)…`
ZINC79090744	0.882	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](OP(=O)(O)O…`
ZINC3871401	0.818	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3871402	0.818	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC3871403	0.818	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3871404	0.818	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC4096223	0.818	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC12501123	0.750	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	0.750	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	0.750	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	0.750	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…`
ZINC12496332	0.741	281.3 Da LogP -1.33 TPSA 128.5	✓ Ro5	✓ Clean	`CO[C@H]1[C@@H](n2cnc3c(N)ncnc32)O[C@H](CO)[C@H]…`
ZINC247825485	0.741	281.3 Da LogP -1.33 TPSA 128.5	✓ Ro5	✓ Clean	`CO[C@@H]1[C@H](O)[C@H](CO)O[C@H]1n1cnc2c(N)ncnc…`
ZINC2617	0.741	281.3 Da LogP -1.33 TPSA 128.5	✓ Ro5	✓ Clean	`CO[C@H]1[C@@H](O)[C@H](CO)O[C@@H]1n1cnc2c(N)ncn…`
ZINC3776540	0.741	281.3 Da LogP -1.33 TPSA 128.5	✓ Ro5	✓ Clean	`CO[C@@H]1[C@H](O)[C@@H](CO)O[C@H]1n1cnc2c(N)ncn…`
ZINC38599716	0.741	281.3 Da LogP -1.33 TPSA 128.5	✓ Ro5	✓ Clean	`CO[C@H]1[C@@H](O)[C@@H](CO)O[C@H]1n1cnc2c(N)ncn…`
ZINC4517830	0.741	281.3 Da LogP -1.33 TPSA 128.5	✓ Ro5	✓ Clean	`CO[C@H]1[C@@H](n2cnc3c(N)ncnc32)O[C@@H](CO)[C@H…`
ZINC4517834	0.741	281.3 Da LogP -1.33 TPSA 128.5	✓ Ro5	✓ Clean	`CO[C@@H]1[C@@H](n2cnc3c(N)ncnc32)O[C@@H](CO)[C@…`
ZINC57416	0.741	281.3 Da LogP -1.33 TPSA 128.5	✓ Ro5	✓ Clean	`CO[C@@H]1[C@@H](O)[C@H](CO)O[C@@H]1n1cnc2c(N)nc…`
ZINC66155294	0.741	281.3 Da LogP -1.33 TPSA 128.5	✓ Ro5	✓ Clean	`CO[C@H]1[C@H](O)[C@@H](CO)O[C@H]1n1cnc2c(N)ncnc…`
ZINC79682528	0.741	281.3 Da LogP -1.33 TPSA 128.5	✓ Ro5	✓ Clean	`CO[C@@H]1[C@@H](O)[C@@H](CO)O[C@H]1n1cnc2c(N)nc…`
ZINC115141587	0.719	325.3 Da LogP -1.31 TPSA 137.8	✓ Ro5	✓ Clean	`COCCO[C@H]1[C@H](O)[C@@H](CO)O[C@H]1n1cnc2c(N)n…`
ZINC15657781	0.719	325.3 Da LogP -1.31 TPSA 137.8	✓ Ro5	✓ Clean	`COCCO[C@@H]1[C@H](O)[C@@H](CO)O[C@H]1n1cnc2c(N)…`
ZINC230402270	0.719	325.3 Da LogP -1.31 TPSA 137.8	✓ Ro5	✓ Clean	`COCCO[C@@H]1[C@@H](O)[C@@H](CO)O[C@@H]1n1cnc2c(…`
ZINC230402277	0.719	325.3 Da LogP -1.31 TPSA 137.8	✓ Ro5	✓ Clean	`COCCO[C@@H]1[C@@H](n2cnc3c(N)ncnc32)O[C@H](CO)[…`
ZINC247880594	0.719	325.3 Da LogP -1.31 TPSA 137.8	✓ Ro5	✓ Clean	`COCCO[C@@H]1[C@H](O)[C@H](CO)O[C@H]1n1cnc2c(N)n…`
ZINC2583383	0.719	325.3 Da LogP -1.31 TPSA 137.8	✓ Ro5	✓ Clean	`COCCO[C@H]1[C@@H](O)[C@H](CO)O[C@@H]1n1cnc2c(N)…`
ZINC44699702	0.719	325.3 Da LogP -1.31 TPSA 137.8	✓ Ro5	✓ Clean	`COCCO[C@H]1[C@@H](O)[C@@H](CO)O[C@H]1n1cnc2c(N)…`
ZINC65743242	0.719	325.3 Da LogP -1.31 TPSA 137.8	✓ Ro5	✓ Clean	`COCCO[C@H]1[C@@H](n2cnc3c(N)ncnc32)O[C@@H](CO)[…`
ZINC83291128	0.719	325.3 Da LogP -1.31 TPSA 137.8	✓ Ro5	✓ Clean	`COCCO[C@@H]1[C@@H](O)[C@@H](CO)O[C@H]1n1cnc2c(N…`
ZINC85475063	0.719	325.3 Da LogP -1.31 TPSA 137.8	✓ Ro5	✓ Clean	`COCCO[C@H]1[C@@H](n2cnc3c(N)ncnc32)O[C@H](CO)[C…`
ZINC90556175	0.719	325.3 Da LogP -1.31 TPSA 137.8	✓ Ro5	✓ Clean	`COCCO[C@H]1[C@@H](O)[C@@H](CO)O[C@@H]1n1cnc2c(N…`
ZINC13549616	0.714	348.2 Da LogP -1.74 TPSA 180.3	✓ Ro5	✓ Clean	`O=P(O)(O)O[C@@H]1[C@@H](CO)O[C@@H](n2cnc3c(O)nc…`
ZINC2047673	0.706	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@H](O)[C@@H]1O`
ZINC2169830	0.706	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O`
ZINC3201878	0.706	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@@H]…`
ZINC3830178	0.706	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@H]1O`
ZINC3978048	0.706	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO)[C@H](O)[C@H]1O`
ZINC8580514	0.706	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](O)[C@@H]1O`
ZINC896706	0.706	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@H](O)[C@H]1O`
ZINC970363	0.706	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O)[C@@H]1O`

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.