Protein profile

KP13_00167

DNA ligase B

Genome: KpKP13

Gene: ligB AHE42087.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3H4K3

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Amino acids 564

Annotations 5

Features 24

PDB binders 7

Druggability 0.836

Overview

Basic information about this protein and its source genome.

Accession: KP13_00167
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: ligB AHE42087.1
Status: annotated
Amino acids: 564
Structure source: AlphaFold + ColabFold

6.5.1.2

GO:0003911 Catalysis of the reaction: NAD+ + deoxyribonucleotide(n) + deoxyribonucleotide(m) = AMP + nicotinamide nucleotide + deoxyribonucleotide(n+m). GO:0006260 The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by the origin recognition complex, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA. GO:0006259 Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides. GO:0006281 The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.

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: CytoplasmicMembrane
ColabFold pLDDT: 90.75

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 0.836

Structure A0A0H3H4K3

Pocket Pocket 1

P2Rank 0.752

Structure A0A0H3H4K3

Pocket Pocket 1

ColabFold model

FPocket 0.822 · Pocket 1

P2Rank 0.824 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 61 / 4744 genomes with a hit

Normalized 0.013

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)

6.5.1.2

Gene Ontology (GO)

GO:0003911 Catalysis of the reaction: NAD+ + deoxyribonucleotide(n) + deoxyribonucleotide(m) = AMP + nicotinamide nucleotide + deoxyribonucleotide(n+m).
GO:0006260 The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by the origin recognition complex, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
GO:0006259 Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
GO:0006281 The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.

Sequence Features

Domain/signature hits from InterPro and related databases.

24 records

Show feature table

Start	End	DB	Term	Name
23	388	PANTHER	PTHR47810	DNA LIGASE
1	25	Phobius	SIGNAL_PEPTIDE	Signal peptide region
21	25	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
30	312	SUPERFAMILY	SSF56091	DNA ligase/mRNA capping enzyme, catalytic domain
317	394	SUPERFAMILY	SSF50249	Nucleic acid-binding proteins
317	394	InterPro	IPR012340	Nucleic acid-binding, OB-fold
34	431	SMART	SM00532	ligaN3
34	431	InterPro	IPR013840	NAD-dependent DNA ligase, N-terminal
95	314	Gene3D	G3DSA:3.30.470.30	DNA ligase/mRNA capping enzyme
117	288	Pfam	PF01653	NAD-dependent DNA ligase adenylation domain
117	288	InterPro	IPR013839	NAD-dependent DNA ligase, adenylation
10	20	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
1	25	SignalP_GRAM_NEGATIVE	SignalP-noTM	SignalP-noTM
26	564	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
406	556	SUPERFAMILY	SSF47781	RuvA domain 2-like
406	556	InterPro	IPR010994	RuvA domain 2-like
12	564	Hamap	MF_01587	DNA ligase B [ligB].
12	564	InterPro	IPR020923	DNA ligase B
32	88	Gene3D	G3DSA:1.10.287.610	Helix hairpin bin
316	400	Gene3D	G3DSA:2.40.50.140	-
316	400	InterPro	IPR012340	Nucleic acid-binding, OB-fold
319	393	Pfam	PF03120	NAD-dependent DNA ligase OB-fold domain
319	393	InterPro	IPR004150	NAD-dependent DNA ligase, OB-fold
1	9	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.

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_A0A0H3H4K3	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_00167	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
1				0.836
25				0.367

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	12.63	0.657
2	11.41	0.61
3	6.48	0.327
4	1.05	0.006
5	0.92	0.004

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				0.822

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	15.61	0.757
2	12.03	0.636
3	7.94	0.422
4	1.13	0.008
5	0.76	0.002

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
0XS	4GLX	P15042	335.1 Da LogP 2.09 TPSA 94.9	✓ Ro5	✓ Clean	`c1c2cc(c(nc2nc(c1C(=O)N)N)C(F)(F)F)Br`
0XT	4GLW	C1CKI0	206.2 Da LogP -0.10 TPSA 112.8	✓ Ro5	✓ Clean	`Cc1c(nc2c(n1)c(nc(n2)N)N)OC`
1X7	4LH6	Q837V6	272.1 Da LogP 1.74 TPSA 82.0	✓ Ro5	✓ Clean	`c1c2c(c(cnc2N)C(=O)N)sc1Br`
1X8	4LH7	Q837V6	236.3 Da LogP 0.08 TPSA 125.1	✓ Ro5	✓ Clean	`c1c2c(c(cnc2N)C(=O)N)sc1C(=O)N`
IVH	3PN1	P43813	355.4 Da LogP -0.09 TPSA 139.5	✓ Ro5	✓ Clean	`CCCCSc1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H…`
IWH	3PN1	P43813	256.3 Da LogP 1.61 TPSA 65.1	✓ Ro5	✓ Clean	`Cc1ccc(c(c1)C)CN2C=C(C=CC2=O)C(=O)N`
NMN	4LH6	Q837V6	335.2 Da LogP -2.20 TPSA 163.4	✓ Ro5	✓ Clean	`c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(…`

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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
CHEMBL1807815	Q9AIU7	6.37	351.4 Da LogP -0.66 TPSA 148.8	✓ Ro5	✓ Clean	`Nc1nc(OC2CCCC2)nc2c1ncn2[C@@H]1O[C@H](CO)[C@@H]…`

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
ZINC12503278	1.000	335.2 Da LogP -2.20 TPSA 163.4	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@@H]2O[C@H](COP(=O)(O)O)[C@@H…`
ZINC1532667	1.000	335.2 Da LogP -2.20 TPSA 163.4	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@H]2O[C@@H](COP(=O)(O)O)[C@H]…`
ZINC2545161	1.000	335.2 Da LogP -2.20 TPSA 163.4	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@@H]2O[C@@H](COP(=O)(O)O)[C@H…`
ZINC3870109	1.000	335.2 Da LogP -2.20 TPSA 163.4	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@@H]2O[C@@H](COP(=O)(O)O)[C@@…`
ZINC40465856	1.000	335.2 Da LogP -2.20 TPSA 163.4	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@@H]2O[C@H](COP(=O)(O)O)[C@H]…`
ZINC40762833	1.000	335.2 Da LogP -2.20 TPSA 163.4	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@H]2O[C@H](COP(=O)(O)O)[C@@H]…`
ZINC4228273	1.000	335.2 Da LogP -2.20 TPSA 163.4	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@@H]2O[C@H](COP(=O)(O)O)[C@@H…`
ZINC77311638	1.000	335.2 Da LogP -2.20 TPSA 163.4	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@@H]2O[C@H](COP(=O)(O)O)[C@H]…`
ZINC4095572	0.809	336.2 Da LogP -1.60 TPSA 157.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc[n+]([C@@H]2O[C@H](COP(=O)(O)O)[C@@H…`
ZINC77311659	0.809	336.2 Da LogP -1.60 TPSA 157.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc[n+]([C@@H]2O[C@H](COP(=O)(O)O)[C@H]…`
ZINC77311660	0.809	336.2 Da LogP -1.60 TPSA 157.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc[n+]([C@@H]2O[C@H](COP(=O)(O)O)[C@H]…`
ZINC77311661	0.809	336.2 Da LogP -1.60 TPSA 157.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc[n+]([C@@H]2O[C@H](COP(=O)(O)O)[C@@H…`
ZINC25756940	0.760	331.3 Da LogP 0.35 TPSA 123.0	✓ Ro5	✓ Clean	`C[C@@H]1[C@@H](COP(=O)(O)O)O[C@@H]([n+]2cccc(C(…`
ZINC13815023	0.722	297.3 Da LogP -1.97 TPSA 148.8	✓ Ro5	✓ Clean	`COc1nc(N)c2ncn([C@@H]3O[C@H](CO)[C@@H](O)[C@H]3…`
ZINC49053484	0.722	297.3 Da LogP -1.97 TPSA 148.8	✓ Ro5	✓ Clean	`COc1nc(N)c2ncn([C@H]3O[C@@H](CO)[C@H](O)[C@@H]3…`
ZINC1776011316	0.700	333.3 Da LogP -1.74 TPSA 154.2	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@@H]2O[C@H](CCP(=O)(O)O)[C@@H…`
ZINC14613564	0.681	255.2 Da LogP -2.32 TPSA 116.9	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@@H]2O[C@H](CO)[C@@H](O)[C@@H…`
ZINC34633968	0.681	255.2 Da LogP -2.32 TPSA 116.9	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@H]2O[C@H](CO)[C@@H](O)[C@H]2…`
ZINC4096036	0.681	255.2 Da LogP -2.32 TPSA 116.9	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@@H]2O[C@H](CO)[C@@H](O)[C@H]…`
ZINC65748069	0.681	255.2 Da LogP -2.32 TPSA 116.9	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@@H]2O[C@H](CO)[C@H](O)[C@H]2…`
ZINC65748073	0.681	255.2 Da LogP -2.32 TPSA 116.9	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@@H]2O[C@H](CO)[C@H](O)[C@@H]…`
ZINC901659	0.681	255.2 Da LogP -2.32 TPSA 116.9	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@H]2O[C@@H](CO)[C@H](O)[C@@H]…`
ZINC105043122	0.660	297.3 Da LogP -2.69 TPSA 177.6	2 viol.	✓ Clean	`NNc1nc(N)c2ncn([C@@H]3O[C@H](CO)[C@H](O)[C@H]3O…`
ZINC12405468	0.660	297.3 Da LogP -2.69 TPSA 177.6	2 viol.	✓ Clean	`NNc1nc(N)c2ncn([C@@H]3O[C@H](CO)[C@@H](O)[C@H]3…`
ZINC14920360	0.660	282.3 Da LogP -2.40 TPSA 165.6	✓ Ro5	✓ Clean	`Nc1nc(N)c2ncn([C@@H]3O[C@H](CO)[C@@H](O)[C@@H]3…`
ZINC17300049	0.660	297.3 Da LogP -2.69 TPSA 177.6	2 viol.	✓ Clean	`NNc1nc(N)c2ncn([C@@H]3O[C@H](CO)[C@@H](O)[C@@H]…`
ZINC1857790181	0.660	299.3 Da LogP -1.69 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1nc(S)nc2c1ncn2[C@H]1O[C@@H](CO)[C@H](O)[C@@H…`
ZINC22048035	0.660	282.3 Da LogP -2.40 TPSA 165.6	✓ Ro5	✓ Clean	`Nc1nc(N)c2ncn([C@@H]3O[C@H](CO)[C@H](O)[C@@H]3O…`
ZINC22048039	0.660	282.3 Da LogP -2.40 TPSA 165.6	✓ Ro5	✓ Clean	`Nc1nc(N)c2ncn([C@@H]3O[C@H](CO)[C@H](O)[C@H]3O)…`
ZINC22060240	0.660	297.3 Da LogP -2.69 TPSA 177.6	2 viol.	✓ Clean	`NNc1nc(N)c2ncn([C@@H]3O[C@H](CO)[C@H](O)[C@@H]3…`
ZINC2383767257	0.660	299.3 Da LogP -1.69 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1nc(S)nc2c1ncn2[C@@H]1O[C@@H](CO)[C@H](O)[C@@…`
ZINC27332328	0.660	282.3 Da LogP -2.40 TPSA 165.6	✓ Ro5	✓ Clean	`Nc1nc(N)c2ncn([C@H]3O[C@@H](CO)[C@H](O)[C@@H]3O…`
ZINC4095498	0.660	282.3 Da LogP -2.40 TPSA 165.6	✓ Ro5	✓ Clean	`Nc1nc(N)c2ncn([C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O…`
ZINC4353413	0.660	282.3 Da LogP -2.40 TPSA 165.6	✓ Ro5	✓ Clean	`Nc1nc(N)c2ncn([C@H]3O[C@@H](CO)[C@@H](O)[C@H]3O…`
ZINC4353414	0.660	282.3 Da LogP -2.40 TPSA 165.6	✓ Ro5	✓ Clean	`Nc1nc(N)c2ncn([C@@H]3O[C@@H](CO)[C@@H](O)[C@H]3…`
ZINC4353415	0.660	282.3 Da LogP -2.40 TPSA 165.6	✓ Ro5	✓ Clean	`Nc1nc(N)c2ncn([C@H]3O[C@@H](CO)[C@@H](O)[C@@H]3…`
ZINC4353416	0.660	282.3 Da LogP -2.40 TPSA 165.6	✓ Ro5	✓ Clean	`Nc1nc(N)c2ncn([C@@H]3O[C@@H](CO)[C@@H](O)[C@@H]…`
ZINC41670453	0.659	257.3 Da LogP 2.21 TPSA 59.3	✓ Ro5	✓ Clean	`Cc1ccc(C)c(Cn2cc(C(=O)O)ccc2=O)c1`
ZINC1661187	0.636	285.2 Da LogP -1.84 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1nc(F)nc2c1ncn2[C@H]1O[C@H](CO)[C@@H](O)[C@@H…`
ZINC19939879	0.636	285.2 Da LogP -1.84 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1nc(F)nc2c1ncn2[C@@H]1O[C@H](CO)[C@H](O)[C@@H…`
ZINC2040952	0.636	285.2 Da LogP -1.84 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1nc(F)nc2c1ncn2[C@H]1O[C@@H](CO)[C@H](O)[C@@H…`
ZINC21982895	0.636	285.2 Da LogP -1.84 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1nc(F)nc2c1ncn2[C@H]1O[C@H](CO)[C@H](O)[C@@H]…`
ZINC22059332	0.636	285.2 Da LogP -1.84 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1nc(F)nc2c1ncn2[C@@H]1O[C@H](CO)[C@H](O)[C@H]…`
ZINC26504975	0.636	393.1 Da LogP -1.38 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1nc(I)nc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@…`
ZINC26504979	0.636	393.1 Da LogP -1.38 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1nc(I)nc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@@…`
ZINC27435623	0.636	393.1 Da LogP -1.38 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1nc(I)nc2c1ncn2[C@@H]1O[C@H](CO)[C@H](O)[C@H]…`
ZINC3875977	0.636	285.2 Da LogP -1.84 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1nc(F)nc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O)[C@H…`
ZINC40455052	0.636	393.1 Da LogP -1.38 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1nc(I)nc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@H…`
ZINC4216238	0.636	285.2 Da LogP -1.84 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1nc(F)nc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O)[C@@…`
ZINC49014899	0.636	393.1 Da LogP -1.38 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1nc(I)nc2c1ncn2[C@H]1O[C@H](CO)[C@@H](O)[C@H]…`

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.