Protein profile

HT085_RS00010

DNA polymerase III subunit beta

Genome: NZ_AP023069.1

Gene: dnaN N776_09345 WHOF_00421 WHOF_00002 ESCNG_30049 TUM19854C_00020 E8M63_03545 Structure source: AlphaFold UniProt A0AA44U8X9 UniProt A0A1D3GQN8

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Amino acids 367

Annotations 6

Features 23

PDB binders 19

Overview

Basic information about this protein and its source genome.

Accession: HT085_RS00010
Assembly: Neisseria gonorrhoeae strain TUM19854 chromosome, complete genome
Gene: dnaN N776_09345 WHOF_00421 WHOF_00002 ESCNG_30049 TUM19854C_00020 E8M63_03545
Status: annotated
Amino acids: 367
Structure source: AlphaFold

GO:0009360 The DNA polymerase III holoenzyme is a complex that contains 10 different types of subunits. These subunits are organized into 3 functionally essential sub-assemblies: the pol III core, the beta sliding clamp processivity factor and the clamp-loading complex. The pol III core carries out the polymerase and the 3'-5' exonuclease proofreading activities. The polymerase is tethered to the template via the sliding clamp processivity factor. The clamp-loading complex assembles the beta processivity factor onto the primer template and plays a central role in the organization and communication at the replication fork. 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:0008408 Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end. GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0006271 The process in which an existing DNA strand is extended by activities including the addition of nucleotides to the 3' end of the strand, complementary to an existing template, as part of DNA replication.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Gut microbiome off-target: hit
Essential (DEG): Y
Localization: Cytoplasmic

Selected Druggability evidence

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 High

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Gene Ontology (GO)

GO:0009360 The DNA polymerase III holoenzyme is a complex that contains 10 different types of subunits. These subunits are organized into 3 functionally essential sub-assemblies: the pol III core, the beta sliding clamp processivity factor and the clamp-loading complex. The pol III core carries out the polymerase and the 3'-5' exonuclease proofreading activities. The polymerase is tethered to the template via the sliding clamp processivity factor. The clamp-loading complex assembles the beta processivity factor onto the primer template and plays a central role in the organization and communication at the replication fork.
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:0008408 Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end.
GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0006271 The process in which an existing DNA strand is extended by activities including the addition of nucleotides to the 3' end of the strand, complementary to an existing template, as part of DNA replication.

Sequence Features

Domain/signature hits from InterPro and related databases.

23 records

Show feature table

Start	End	DB	Term	Name
2	367	PIRSF	PIRSF000804	DNA_pol_III_b
2	367	InterPro	IPR001001	DNA polymerase III, beta sliding clamp
5	243	Gene3D	G3DSA:3.10.150.10	DNA Polymerase III, subunit A, domain 2
139	365	Gene3D	G3DSA:3.70.10.10	-
5	117	SUPERFAMILY	SSF55979	DNA clamp
5	117	InterPro	IPR046938	DNA clamp superfamily
247	366	Pfam	PF02768	DNA polymerase III beta subunit, C-terminal domain
247	366	InterPro	IPR022635	DNA polymerase III, beta sliding clamp, C-terminal
5	119	Pfam	PF00712	DNA polymerase III beta subunit, N-terminal domain
5	119	InterPro	IPR022634	DNA polymerase III, beta sliding clamp, N-terminal
246	367	SUPERFAMILY	SSF55979	DNA clamp
246	367	InterPro	IPR046938	DNA clamp superfamily
4	366	NCBIfam	TIGR00663	DNA polymerase III subunit beta
4	366	InterPro	IPR001001	DNA polymerase III, beta sliding clamp
4	366	CDD	cd00140	beta_clamp
131	244	Pfam	PF02767	DNA polymerase III beta subunit, central domain
131	244	InterPro	IPR022637	DNA polymerase III, beta sliding clamp, central
128	245	SUPERFAMILY	SSF55979	DNA clamp
128	245	InterPro	IPR046938	DNA clamp superfamily
5	367	PANTHER	PTHR30478	DNA POLYMERASE III SUBUNIT BETA
5	367	InterPro	IPR001001	DNA polymerase III, beta sliding clamp
18	363	SMART	SM00480	pol35
18	363	InterPro	IPR001001	DNA polymerase III, beta sliding clamp

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

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Structural evidence

0 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold HT085_RS00010	AlphaFold	—	—	full sequence	—	Viewing

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
5				0.409
3				0.217

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	2.36	0.05
2	1.22	0.01
3	0.81	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.

74 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
0LA	5FXT	O25242	273.7 Da LogP 4.16 TPSA 53.1	✓ Ro5	✓ Clean	`C[C@@H](c1ccc2c3cc(ccc3[nH]c2c1)Cl)C(=O)O`
1FL	5G48	O25242	250.2 Da LogP 3.04 TPSA 57.5	✓ Ro5	✓ Clean	`c1cc(c(cc1c2ccc(cc2F)F)C(=O)O)O`
27O	4MJP	P0A988	282.4 Da LogP 5.08 TPSA 37.3	1 viol.	✓ Clean	`C[C@H](c1ccc(c2c1cccc2)C3CCCCC3)C(=O)O`
27R	4MJQ	P0A988	334.2 Da LogP 2.89 TPSA 80.4	✓ Ro5	Alert	`c1cc(c(c(c1)C(=O)c2ccc(cc2)Br)N)CC(=O)O`
2HO	4N94	P0A988	157.1 Da LogP 1.06 TPSA 43.1	✓ Ro5	✓ Clean	`c1cc(c(cc1C(=O)N)F)F`
2HQ	4N95	P0A988	181.6 Da LogP 1.47 TPSA 46.2	✓ Ro5	✓ Clean	`c1cc2c(cc1Cl)C(=O)C(=O)N2`
2HU	4N97	P0A988	162.1 Da LogP 2.08 TPSA 58.9	✓ Ro5	✓ Clean	`c1cc2c(cc[nH]2)cc1[N+](=O)[O-]`
2J1	4N99	P0A988	249.7 Da LogP 3.40 TPSA 53.1	✓ Ro5	Alert	`c1c2c(cc(c1Cl)C(=O)O)[nH]c3c2CCCC3`
2J2	4N9A	P0A988	249.7 Da LogP 3.33 TPSA 53.1	✓ Ro5	✓ Clean	`c1cc2c(cc1Cl)c3c([nH]2)[C@@H](CCC3)C(=O)O`
322	3D1G	P0A988	499.2 Da LogP 3.17 TPSA 87.1	✓ Ro5	Alert	`CCOc1cc(c(c(c1O)Br)Br)C[C@@H]2C(=O)N(C(=S)S2)CC…`
323	3D1F	P0A988	414.5 Da LogP 2.48 TPSA 76.6	✓ Ro5	✓ Clean	`CN(C)c1ccc2c(c1)OC3=CC(=[N+](C)C)C=CC3=C2c4ccc(…`
4FC	4N98	P0A988	216.2 Da LogP 3.19 TPSA 37.3	✓ Ro5	✓ Clean	`c1cc(ccc1c2ccc(cc2)F)C(=O)O`
5CY	3BEP	P0A988	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…`
6NI	4N96	P0A988	163.1 Da LogP 1.47 TPSA 71.8	✓ Ro5	✓ Clean	`c1cc2cn[nH]c2cc1[N+](=O)[O-]`
743	3QSB	P0A988	434.5 Da LogP 5.49 TPSA 79.5	1 viol.	✓ Clean	`CCCC(=NOCc1ccc(cc1)c2ccc(cc2)F)C3C(=O)CC(C(C3=O…`
BU3	5AGV	P9WNU1	90.1 Da LogP -0.25 TPSA 40.5	✓ Ro5	✓ Clean	`C[C@H]([C@@H](C)O)O`
MLU	5AGU	P9WNU1	145.2 Da LogP 0.71 TPSA 49.3	✓ Ro5	✓ Clean	`CC(C)C[C@H](C(=O)O)NC`
P4C	4K3S	P0A988	324.4 Da LogP -0.72 TPSA 92.7	✓ Ro5	✓ Clean	`C(COCCOCCOCCOCCOCCOCC=O)O`
SFK	4K3K	P0A988	263.3 Da LogP 2.23 TPSA 66.4	✓ Ro5	✓ Clean	`CC(C)CCC(=O)N[C@@H](Cc1ccccc1)C(=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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
CHEMBL3577268	P0A988	—	249.7 Da LogP 3.01 TPSA 53.1	✓ Ro5	Alert	`O=C(O)[C@@H]1CCc2c([nH]c3ccc(Cl)cc23)C1`
CHEMBL3577269	P0A988	—	249.7 Da LogP 3.01 TPSA 53.1	✓ Ro5	Alert	`O=C(O)[C@H]1CCc2c([nH]c3ccc(Cl)cc23)C1`
CHEMBL3577272	P0A988	—	294.1 Da LogP 3.12 TPSA 53.1	✓ Ro5	Alert	`O=C(O)[C@@H]1CCc2c([nH]c3ccc(Br)cc23)C1`
CHEMBL3577289	P0A988	—	499.4 Da LogP 3.41 TPSA 108.6	✓ Ro5	Alert	`O=C(Cn1c2c(c3cc(Br)ccc31)CC[C@@H](C(=O)O)C2)N[C…`
CHEMBL3577290	P0A988	—	499.4 Da LogP 3.41 TPSA 108.6	✓ Ro5	Alert	`O=C(Cn1c2c(c3cc(Br)ccc31)CC[C@@H](C(=O)O)C2)N[C…`

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
ZINC117391805	1.000	294.1 Da LogP 3.12 TPSA 53.1	✓ Ro5	Alert	`O=C(O)[C@@H]1CCc2c([nH]c3ccc(Br)cc23)C1`
ZINC117391807	1.000	294.1 Da LogP 3.12 TPSA 53.1	✓ Ro5	Alert	`O=C(O)[C@H]1CCc2c([nH]c3ccc(Br)cc23)C1`
ZINC12501520	1.000	458.5 Da LogP -0.88 TPSA 123.5	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1869694	1.000	273.7 Da LogP 4.16 TPSA 53.1	✓ Ro5	✓ Clean	`C[C@@H](C(=O)O)c1ccc2c(c1)[nH]c1ccc(Cl)cc12`
ZINC20235	1.000	273.7 Da LogP 4.16 TPSA 53.1	✓ Ro5	✓ Clean	`C[C@H](C(=O)O)c1ccc2c(c1)[nH]c1ccc(Cl)cc12`
ZINC20243	1.000	250.2 Da LogP 3.04 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1cc(-c2ccc(F)cc2F)ccc1O`
ZINC2382451	1.000	216.2 Da LogP 3.19 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(F)cc2)cc1`
ZINC2570817	1.000	334.2 Da LogP 2.89 TPSA 80.4	✓ Ro5	Alert	`Nc1c(CC(=O)O)cccc1C(=O)c1ccc(Br)cc1`
ZINC340258	1.000	249.7 Da LogP 3.33 TPSA 53.1	✓ Ro5	✓ Clean	`O=C(O)[C@H]1CCCc2c1[nH]c1ccc(Cl)cc21`
ZINC3874716	1.000	414.5 Da LogP -0.90 TPSA 114.3	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC4018831	1.000	249.7 Da LogP 3.33 TPSA 53.1	✓ Ro5	✓ Clean	`O=C(O)[C@@H]1CCCc2c1[nH]c1ccc(Cl)cc21`
ZINC4283769	1.000	238.3 Da LogP -0.96 TPSA 77.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCO`
ZINC4521548	1.000	282.3 Da LogP -0.95 TPSA 86.6	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCO`
ZINC5178829	1.000	326.4 Da LogP -0.93 TPSA 95.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCO`
ZINC5178830	1.000	370.4 Da LogP -0.91 TPSA 105.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC807911	1.000	249.7 Da LogP 3.40 TPSA 53.1	✓ Ro5	Alert	`O=C(O)c1cc2[nH]c3c(c2cc1Cl)CCCC3`
ZINC575319668	0.923	263.7 Da LogP 3.72 TPSA 53.1	✓ Ro5	✓ Clean	`O=C(O)[C@H]1CCCCc2c1[nH]c1ccc(Cl)cc21`
ZINC575319669	0.923	263.7 Da LogP 3.72 TPSA 53.1	✓ Ro5	✓ Clean	`O=C(O)[C@@H]1CCCCc2c1[nH]c1ccc(Cl)cc21`
ZINC49837746	0.810	249.7 Da LogP 3.01 TPSA 53.1	✓ Ro5	Alert	`O=C(O)[C@H]1CCc2[nH]c3ccc(Cl)cc3c2C1`
ZINC49837747	0.810	249.7 Da LogP 3.01 TPSA 53.1	✓ Ro5	Alert	`O=C(O)[C@@H]1CCc2[nH]c3ccc(Cl)cc3c2C1`
ZINC93985	0.786	248.7 Da LogP 2.73 TPSA 58.9	✓ Ro5	✓ Clean	`NC(=O)[C@H]1CCCc2c1[nH]c1ccc(Cl)cc21`
ZINC93989	0.786	248.7 Da LogP 2.73 TPSA 58.9	✓ Ro5	✓ Clean	`NC(=O)[C@@H]1CCCc2c1[nH]c1ccc(Cl)cc21`
ZINC909	0.765	255.3 Da LogP 2.13 TPSA 80.4	✓ Ro5	Alert	`Nc1c(CC(=O)O)cccc1C(=O)c1ccccc1`
ZINC134079	0.750	242.2 Da LogP 2.75 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(C(=O)O)cc2)cc1`
ZINC3147211	0.750	318.3 Da LogP 4.42 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(-c3ccc(C(=O)O)cc3)cc2)cc1`
ZINC15261553	0.737	294.3 Da LogP -0.01 TPSA 129.7	✓ Ro5	✓ Clean	`N[C@H](CCC(=O)N[C@@H](Cc1ccccc1)C(=O)O)C(=O)O`
ZINC15261555	0.737	294.3 Da LogP -0.01 TPSA 129.7	✓ Ro5	✓ Clean	`N[C@@H](CCC(=O)N[C@H](Cc1ccccc1)C(=O)O)C(=O)O`
ZINC15261557	0.737	294.3 Da LogP -0.01 TPSA 129.7	✓ Ro5	✓ Clean	`N[C@H](CCC(=O)N[C@H](Cc1ccccc1)C(=O)O)C(=O)O`
ZINC2242693	0.737	294.3 Da LogP -0.01 TPSA 129.7	✓ Ro5	✓ Clean	`N[C@@H](CCC(=O)N[C@@H](Cc1ccccc1)C(=O)O)C(=O)O`
ZINC16946243	0.733	257.7 Da LogP 3.14 TPSA 46.2	✓ Ro5	✓ Clean	`O=C1Nc2ccc(-c3ccc(Cl)cc3)cc2C1=O`
ZINC53542	0.733	263.7 Da LogP 3.41 TPSA 42.1	✓ Ro5	✓ Clean	`COC(=O)[C@H]1CCCc2c1[nH]c1ccc(Cl)cc21`
ZINC53543	0.733	263.7 Da LogP 3.41 TPSA 42.1	✓ Ro5	✓ Clean	`COC(=O)[C@@H]1CCCc2c1[nH]c1ccc(Cl)cc21`
ZINC5161668	0.730	289.7 Da LogP 2.78 TPSA 80.4	✓ Ro5	Alert	`Nc1c(CC(=O)O)cccc1C(=O)c1ccc(Cl)cc1`
ZINC499303	0.727	262.7 Da LogP 3.12 TPSA 58.9	✓ Ro5	✓ Clean	`NC(=O)[C@H]1CCCCc2c1[nH]c1ccc(Cl)cc21`
ZINC499304	0.727	262.7 Da LogP 3.12 TPSA 58.9	✓ Ro5	✓ Clean	`NC(=O)[C@@H]1CCCCc2c1[nH]c1ccc(Cl)cc21`
ZINC1598043	0.722	236.3 Da LogP 0.15 TPSA 92.4	✓ Ro5	✓ Clean	`NCCC(=O)N[C@H](Cc1ccccc1)C(=O)O`
ZINC1845204	0.722	297.4 Da LogP 2.43 TPSA 66.4	✓ Ro5	✓ Clean	`O=C(CCc1ccccc1)N[C@H](Cc1ccccc1)C(=O)O`
ZINC1845206	0.722	297.4 Da LogP 2.43 TPSA 66.4	✓ Ro5	✓ Clean	`O=C(CCc1ccccc1)N[C@@H](Cc1ccccc1)C(=O)O`
ZINC2545129	0.722	236.3 Da LogP 0.15 TPSA 92.4	✓ Ro5	✓ Clean	`NCCC(=O)N[C@@H](Cc1ccccc1)C(=O)O`
ZINC3175547	0.722	265.3 Da LogP 0.66 TPSA 103.7	✓ Ro5	✓ Clean	`O=C(O)CCC(=O)N[C@@H](Cc1ccccc1)C(=O)O`
ZINC3175549	0.722	265.3 Da LogP 0.66 TPSA 103.7	✓ Ro5	✓ Clean	`O=C(O)CCC(=O)N[C@H](Cc1ccccc1)C(=O)O`
ZINC128690	0.721	294.1 Da LogP 3.43 TPSA 53.1	✓ Ro5	✓ Clean	`O=C(O)[C@H]1CCCc2c1[nH]c1ccc(Br)cc21`
ZINC128692	0.721	294.1 Da LogP 3.43 TPSA 53.1	✓ Ro5	✓ Clean	`O=C(O)[C@@H]1CCCc2c1[nH]c1ccc(Br)cc21`
ZINC3683849	0.721	229.3 Da LogP 2.98 TPSA 53.1	✓ Ro5	✓ Clean	`Cc1ccc2[nH]c3c(c2c1)CCC[C@@H]3C(=O)O`
ZINC3683850	0.721	229.3 Da LogP 2.98 TPSA 53.1	✓ Ro5	✓ Clean	`Cc1ccc2[nH]c3c(c2c1)CCC[C@H]3C(=O)O`
ZINC2513032	0.720	234.2 Da LogP 3.33 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2cc(F)cc(F)c2)cc1`
ZINC1677646	0.714	221.3 Da LogP 1.21 TPSA 66.4	✓ Ro5	✓ Clean	`CCC(=O)N[C@@H](Cc1ccccc1)C(=O)O`
ZINC38068703	0.714	252.2 Da LogP 3.47 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(F)cc2F)cc1F`
ZINC6655209	0.714	221.3 Da LogP 1.21 TPSA 66.4	✓ Ro5	✓ Clean	`CCC(=O)N[C@H](Cc1ccccc1)C(=O)O`
ZINC22054172	0.711	301.8 Da LogP 4.64 TPSA 42.1	✓ Ro5	✓ Clean	`CCOC(=O)[C@@H](C)c1ccc2c(c1)[nH]c1ccc(Cl)cc12`

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.