Protein profile

KP13_01945

DNA polymerase II

Genome: KpKP13

Gene: AHE46384.1 polB Structure source: AlphaFold + ColabFold UniProt A0A0H3GI42

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Amino acids 785

Annotations 8

Features 38

PDB binders 14

Druggability 0.325

Overview

Basic information about this protein and its source genome.

Accession: KP13_01945
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE46384.1 polB
Status: annotated
Amino acids: 785
Structure source: AlphaFold + ColabFold

2.7.7.7

GO:0003676 Binding to a nucleic acid. GO:0003887 Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); DNA-template-directed extension of the 3'-end of a DNA strand by one nucleotide at a time. 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. GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). GO:0008296 Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of a DNA molecule. GO:0045004 Correction of replication errors by DNA polymerase using a 3'-5' exonuclease activity.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 27.636
Human E-value: 1.95e-08
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 93.5

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 0.325

Structure A0A0H3GI42

Pocket Pocket 60

P2Rank 0.337

Structure A0A0H3GI42

Pocket Pocket 1

ColabFold model

FPocket 0.651 · Pocket 48

P2Rank 0.606 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 130 / 4744 genomes with a hit

Normalized 0.027

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

2.7.7.7

Gene Ontology (GO)

GO:0003676 Binding to a nucleic acid.
GO:0003887 Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); DNA-template-directed extension of the 3'-end of a DNA strand by one nucleotide at a time.
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.
GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
GO:0008296 Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of a DNA molecule.
GO:0045004 Correction of replication errors by DNA polymerase using a 3'-5' exonuclease activity.
GO:0009432 An error-prone process for repairing damaged microbial DNA.

Sequence Features

Domain/signature hits from InterPro and related databases.

38 records

Show feature table

Start	End	DB	Term	Name
2	46	FunFam	G3DSA:2.40.50.590:FF:000001	DNA polymerase
350	448	Gene3D	G3DSA:3.90.1600.10	Palm domain of DNA polymerase
350	448	InterPro	IPR023211	DNA polymerase, palm domain superfamily
449	640	Gene3D	G3DSA:3.90.1600.10	Palm domain of DNA polymerase
449	640	InterPro	IPR023211	DNA polymerase, palm domain superfamily
2	80	Gene3D	G3DSA:2.40.50.590	-
91	152	Gene3D	G3DSA:2.40.50.590	-
383	433	Pfam	PF00136	DNA polymerase family B
383	433	InterPro	IPR006134	DNA-directed DNA polymerase, family B, multifunctional domain
491	740	Pfam	PF00136	DNA polymerase family B
491	740	InterPro	IPR006134	DNA-directed DNA polymerase, family B, multifunctional domain
206	298	Pfam	PF03104	DNA polymerase family B, exonuclease domain
206	298	InterPro	IPR006133	DNA-directed DNA polymerase, family B, exonuclease domain
75	776	PANTHER	PTHR10322	DNA POLYMERASE CATALYTIC SUBUNIT
543	551	PRINTS	PR00106	DNA-directed DNA-polymerase family B signature
543	551	InterPro	IPR006172	DNA-directed DNA polymerase, family B
491	503	PRINTS	PR00106	DNA-directed DNA-polymerase family B signature
491	503	InterPro	IPR006172	DNA-directed DNA polymerase, family B
417	430	PRINTS	PR00106	DNA-directed DNA-polymerase family B signature
417	430	InterPro	IPR006172	DNA-directed DNA polymerase, family B
545	553	ProSitePatterns	PS00116	DNA polymerase family B signature.
545	553	InterPro	IPR017964	DNA-directed DNA polymerase, family B, conserved site
150	346	CDD	cd05784	DNA_polB_II_exo
350	448	FunFam	G3DSA:3.90.1600.10:FF:000009	DNA polymerase
153	349	Gene3D	G3DSA:3.30.420.10	-
153	349	InterPro	IPR036397	Ribonuclease H superfamily
387	779	SUPERFAMILY	SSF56672	DNA/RNA polymerases
387	779	InterPro	IPR043502	DNA/RNA polymerase superfamily
399	771	CDD	cd05537	POLBc_Pol_II
641	785	Gene3D	G3DSA:1.10.132.60	-
641	785	InterPro	IPR042087	DNA polymerase family B, thumb domain
641	785	FunFam	G3DSA:1.10.132.60:FF:000008	DNA polymerase
150	557	SMART	SM00486	polmehr3
150	557	InterPro	IPR006172	DNA-directed DNA polymerase, family B
6	391	SUPERFAMILY	SSF53098	Ribonuclease H-like
6	391	InterPro	IPR012337	Ribonuclease H-like superfamily
451	640	FunFam	G3DSA:3.90.1600.10:FF:000010	DNA polymerase
153	349	FunFam	G3DSA:3.30.420.10:FF:000052	DNA polymerase

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_A0A0H3GI42	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_01945	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
60				0.325
28				0.28
26				0.232

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	6.28	0.315
2	3.81	0.147
3	3.76	0.144
4	3.54	0.13
5	2.94	0.094

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
48				0.651

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	10.16	0.547
2	6.43	0.324
3	4.35	0.181
4	4.18	0.17
5	3.48	0.127

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.

64 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
5CY	4K8X	Q56366	471.7 Da LogP 5.62 TPSA 46.7	1 viol.	✓ Clean	`CC1(c2ccccc2[N+](=C1/C=C/C=C/C=C/3\C(c4ccccc4N3…`
9O7	5VU8	D0VWU9	477.2 Da LogP -0.99 TPSA 258.9	2 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@H](CO3)OP(=O)…`
B0U	6ISI	Q56366	221.3 Da LogP -0.53 TPSA 91.0	✓ Ro5	✓ Clean	`C(COCCOCCOCCN)C(=O)O`
B9X	6ISH	Q56366	475.4 Da LogP 0.16 TPSA 190.4	1 viol.	✓ Clean	`CCOCCOCCC(=O)O[C@H]1C[C@@H](O[C@@H]1COP(=O)(O)O…`
DCP	3K59	P21189	467.2 Da LogP -1.18 TPSA 250.2	2 viol.	✓ Clean	`C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)CO[P@@](=…`
DG	6S1M	P28340	347.2 Da LogP -1.54 TPSA 185.8	✓ Ro5	✓ Clean	`c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N…`
DG3	3K5M	P21189	491.2 Da LogP -0.28 TPSA 258.6	2 viol.	✓ Clean	`c1nc2c(n1[C@H]3CC[C@H](O3)CO[P@@](=O)(O)O[P@](=…`
DGT	3MAQ	P21189	507.2 Da LogP -1.31 TPSA 278.9	3 viol.	✓ Clean	`c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)CO[P@@](=O)(O)O…`
DTP	5OMQ	Q56366	491.2 Da LogP -0.60 TPSA 258.9	2 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)CO[P@]…`
DZ4	6WYA	D0VWU9	490.2 Da LogP -1.03 TPSA 261.7	2 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)CO[P@@…`
FA2	5VU7	D0VWU9	317.2 Da LogP -1.22 TPSA 165.8	✓ Ro5	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@H](CO3)OP(=O)…`
PPV	6ISG	Q56366	178.0 Da LogP -0.81 TPSA 124.3	✓ Ro5	✓ Clean	`OP(=O)(O)OP(=O)(O)O`
TCE	6WYB	D0VWU9	250.2 Da LogP 0.89 TPSA 111.9	✓ Ro5	✓ Clean	`C(CP(CCC(=O)O)CCC(=O)O)C(=O)O`
TTP	6S1M	P28340	482.2 Da LogP -1.16 TPSA 244.1	2 viol.	✓ Clean	`CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@]…`

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
ZINC12296728	1.000	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)…`
ZINC13507072	1.000	482.2 Da LogP -1.16 TPSA 244.1	2 viol.	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@H](CO[P@@](=O)(O)O[P@…`
ZINC13527599	1.000	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	1.000	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	1.000	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	1.000	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…`
ZINC2517013	1.000	250.2 Da LogP 0.89 TPSA 111.9	✓ Ro5	✓ Clean	`O=C(O)CCP(CCC(=O)O)CCC(=O)O`
ZINC33979251	1.000	482.2 Da LogP -1.16 TPSA 244.1	2 viol.	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@H](CO[P@@](=O)(O)O[P@@…`
ZINC35923817	1.000	221.3 Da LogP -0.53 TPSA 91.0	✓ Ro5	✓ Clean	`NCCOCCOCCOCCC(=O)O`
ZINC3869846	1.000	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	1.000	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	1.000	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…`
ZINC71257139	1.000	353.4 Da LogP -0.48 TPSA 118.7	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCC(=O)O`
ZINC79016460	1.000	265.3 Da LogP -0.51 TPSA 100.2	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCC(=O)O`
ZINC83253934	1.000	441.5 Da LogP -0.45 TPSA 137.2	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCOCCC(=O)O`
ZINC96024082	1.000	309.4 Da LogP -0.50 TPSA 109.5	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCC(=O)O`
ZINC96034819	1.000	397.5 Da LogP -0.46 TPSA 127.9	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCC(=O)O`
ZINC96503485	1.000	485.6 Da LogP -0.43 TPSA 146.4	1 viol.	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCOCCOCCC(=O)O`
ZINC12503053	0.959	402.2 Da LogP -1.28 TPSA 197.6	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC33979243	0.959	402.2 Da LogP -1.28 TPSA 197.6	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC33979244	0.959	402.2 Da LogP -1.28 TPSA 197.6	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](O)[C@H](CO[P@@](=O)(O)OP(=O)…`
ZINC33979245	0.959	402.2 Da LogP -1.28 TPSA 197.6	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@H](CO[P@@](=O)(O)OP(=…`
ZINC33979246	0.959	402.2 Da LogP -1.28 TPSA 197.6	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@@H](O)[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC8215882	0.959	402.2 Da LogP -1.28 TPSA 197.6	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](O)[C@@H](CO[P@@](=O)(O)OP(=O…`
ZINC12503703	0.860	427.2 Da LogP -1.42 TPSA 232.3	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2C[C@H](O)[C@@H](CO[P@@](=O)(…`
ZINC8215878	0.860	427.2 Da LogP -1.42 TPSA 232.3	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2C[C@H](O)[C@@H](CO[P@@](=O)(O…`
ZINC111459735	0.836	481.2 Da LogP -1.20 TPSA 249.9	2 viol.	✓ Clean	`Cc1cn([C@@H]2C[C@H](N)[C@H](CO[P@@](=O)(O)O[P@@…`
ZINC138164075	0.836	498.2 Da LogP 0.21 TPSA 227.1	2 viol.	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@H](CO[P@@](=O)(O)O[P@@…`
ZINC142512519	0.818	498.2 Da LogP 0.21 TPSA 227.1	2 viol.	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@H](CO[P@@](=O)(O)O[P@@…`
ZINC13523519	0.804	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@@H](COP(=O)(O)O)O2)c(…`
ZINC1532628	0.804	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@H](COP(=O)(O)O)O2)c(=…`
ZINC1678872	0.804	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](O)[C@@H](COP(=O)(O)O)O2)c(=O…`
ZINC2047010	0.804	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@@H](O)[C@H](COP(=O)(O)O)O2)c(=O…`
ZINC3870253	0.804	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@H](COP(=O)(O)O)O2)c(=O…`
ZINC3870254	0.804	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](O)[C@H](COP(=O)(O)O)O2)c(=O)…`
ZINC6523446	0.804	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@@H](COP(=O)(O)O)O2)c(=…`
ZINC113218151	0.800	486.1 Da LogP -1.33 TPSA 244.1	2 viol.	✓ Clean	`O=c1[nH]c(=O)n([C@H]2C[C@H](O)[C@@H](CO[P@](=O)…`
ZINC80168152	0.800	486.1 Da LogP -1.33 TPSA 244.1	2 viol.	✓ Clean	`O=c1[nH]c(=O)n([C@@H]2C[C@H](O)[C@H](CO[P@@](=O…`
ZINC59206718	0.786	498.2 Da LogP -1.98 TPSA 264.4	2 viol.	✓ Clean	`O=c1[nH]c(=O)n([C@@H]2C[C@H](O)[C@H](CO[P@@](=O…`
ZINC138954515	0.772	496.2 Da LogP -1.66 TPSA 261.2	2 viol.	✓ Clean	`O=Cc1cn([C@@H]2C[C@H](O)[C@H](CO[P@@](=O)(O)O[P…`
ZINC1542984448	0.750	470.5 Da LogP 0.07 TPSA 148.4	✓ Ro5	✓ Clean	`O=C(O)CCOCCOCCOCCOCCOCCOCCOCCOCCC(=O)O`
ZINC201768036	0.750	279.3 Da LogP -0.12 TPSA 100.2	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCCC(=O)O`
ZINC31298140	0.750	498.2 Da LogP -2.19 TPSA 264.4	2 viol.	✓ Clean	`Cc1cn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(O)…`
ZINC35977596	0.750	294.3 Da LogP 0.00 TPSA 111.5	✓ Ro5	✓ Clean	`O=C(O)CCOCCOCCOCCOCCC(=O)O`
ZINC39383060	0.750	206.2 Da LogP -0.03 TPSA 93.1	✓ Ro5	✓ Clean	`O=C(O)CCOCCOCCC(=O)O`
ZINC39427081	0.750	250.2 Da LogP -0.01 TPSA 102.3	✓ Ro5	✓ Clean	`O=C(O)CCOCCOCCOCCC(=O)O`
ZINC71257127	0.750	426.5 Da LogP 0.05 TPSA 139.2	✓ Ro5	✓ Clean	`O=C(O)CCOCCOCCOCCOCCOCCOCCOCCC(=O)O`
ZINC71257128	0.750	338.4 Da LogP 0.02 TPSA 120.8	✓ Ro5	✓ Clean	`O=C(O)CCOCCOCCOCCOCCOCCC(=O)O`
ZINC79016464	0.750	382.4 Da LogP 0.04 TPSA 130.0	✓ Ro5	✓ Clean	`O=C(O)CCOCCOCCOCCOCCOCCOCCC(=O)O`
ZINC81168756	0.750	498.2 Da LogP -2.19 TPSA 264.4	2 viol.	✓ Clean	`Cc1cn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(O)…`

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.