Protein profile

KP13_03949

UvrABC system protein B

Genome: KpKP13

Gene: AHE47461.1 Structure source: AlphaFold + ColabFold UniProt A0A1J0QZW6

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Amino acids 658

Annotations 7

Features 33

PDB binders 6

Druggability 0.495

Overview

Basic information about this protein and its source genome.

Accession: KP13_03949
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE47461.1
Status: annotated
Amino acids: 658
Structure source: AlphaFold + ColabFold

GO:0016887 Catalysis of the reaction: ATP + H2O = ADP + H+ phosphate. ATP hydrolysis is used in some reactions as an energy source, for example to catalyze a reaction or drive transport against a concentration gradient. GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. GO:0006289 A DNA repair process in which a small region of the strand surrounding the damage is removed from the DNA helix as an oligonucleotide. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. Nucleotide excision repair recognizes a wide range of substrates, including damage caused by UV irradiation (pyrimidine dimers and 6-4 photoproducts) and chemicals (intrastrand cross-links and bulky adducts). GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0009380 Any of the protein complexes formed by the UvrABC excinuclease system, which carries out nucleotide excision repair. Three different complexes are formed by the 3 proteins as they proceed through the excision repair process. First a complex consisting of two A subunits and two B subunits bind DNA and unwind it around the damaged site. Then, the A subunits disassociate leaving behind a stable complex between B subunits and DNA. Now, subunit C binds to this B+DNA complex and causes subunit B to nick the DNA on one side of the complex while subunit C nicks the DNA on the other side of the complex. DNA polymerase I and DNA ligase can then repair the resulting gap. GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 29.87
Human E-value: 5.15e-07
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 58.092
DEG E-value: 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 87.59

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 0.495

Structure A0A1J0QZW6

Pocket Pocket 8

P2Rank 0.887

Structure A0A1J0QZW6

Pocket Pocket 1

ColabFold model

FPocket 0.994 · Pocket 3

P2Rank 0.914 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 3697 / 4744 genomes with a hit

Normalized 0.779

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

7 GO

Gene Ontology (GO)

GO:0016887 Catalysis of the reaction: ATP + H2O = ADP + H+ phosphate. ATP hydrolysis is used in some reactions as an energy source, for example to catalyze a reaction or drive transport against a concentration gradient.
GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
GO:0006289 A DNA repair process in which a small region of the strand surrounding the damage is removed from the DNA helix as an oligonucleotide. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. Nucleotide excision repair recognizes a wide range of substrates, including damage caused by UV irradiation (pyrimidine dimers and 6-4 photoproducts) and chemicals (intrastrand cross-links and bulky adducts).
GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
GO:0009380 Any of the protein complexes formed by the UvrABC excinuclease system, which carries out nucleotide excision repair. Three different complexes are formed by the 3 proteins as they proceed through the excision repair process. First a complex consisting of two A subunits and two B subunits bind DNA and unwind it around the damaged site. Then, the A subunits disassociate leaving behind a stable complex between B subunits and DNA. Now, subunit C binds to this B+DNA complex and causes subunit B to nick the DNA on one side of the complex while subunit C nicks the DNA on the other side of the complex. DNA polymerase I and DNA ligase can then repair the resulting gap.
GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
GO:0004518 Catalysis of the cleavage of ester linkages within nucleic acids.

Sequence Features

Domain/signature hits from InterPro and related databases.

33 records

Show feature table

Start	End	DB	Term	Name
38	588	SUPERFAMILY	SSF52540	P-loop containing nucleoside triphosphate hydrolases
38	588	InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase
252	415	Gene3D	G3DSA:3.40.50.300	-
252	415	InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase
5	245	Gene3D	G3DSA:3.40.50.300	-
5	245	InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase
163	250	Pfam	PF17757	UvrB interaction domain
163	250	InterPro	IPR041471	UvrB, interaction domain
416	591	Gene3D	G3DSA:3.40.50.300	-
416	591	InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase
5	652	NCBIfam	TIGR00631	excinuclease ABC subunit UvrB
5	652	InterPro	IPR004807	UvrABC system, subunit B
634	654	Coils	Coil	Coil
6	416	SUPERFAMILY	SSF52540	P-loop containing nucleoside triphosphate hydrolases
6	416	InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase
553	593	Pfam	PF12344	Ultra-violet resistance protein B
553	593	InterPro	IPR024759	UvrB, YAD/RRR-motif-containing domain
428	596	ProSiteProfiles	PS51194	Superfamilies 1 and 2 helicase C-terminal domain profile.
428	596	InterPro	IPR001650	Helicase, C-terminal
265	301	Coils	Coil	Coil
27	160	ProSiteProfiles	PS51192	Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile.
27	160	InterPro	IPR014001	Helicase superfamily 1/2, ATP-binding domain
17	88	Pfam	PF04851	Type III restriction enzyme, res subunit
17	88	InterPro	IPR006935	Helicase/UvrB, N-terminal
10	427	SMART	SM00487	ultradead3
10	427	InterPro	IPR014001	Helicase superfamily 1/2, ATP-binding domain
5	612	PANTHER	PTHR24029	UVRABC SYSTEM PROTEIN B
5	612	InterPro	IPR004807	UvrABC system, subunit B
434	545	Pfam	PF00271	Helicase conserved C-terminal domain
434	545	InterPro	IPR001650	Helicase, C-terminal
461	547	SMART	SM00490	helicmild6
461	547	InterPro	IPR001650	Helicase, C-terminal
6	415	CDD	cd17916	DEXHc_UvrB

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_A0A1J0QZW6	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_03949	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
8				0.495
43				0.415

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	18.68	0.827
2	13.54	0.69
3	6.43	0.324
4	2.5	0.069
5	1.75	0.032

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				0.994
43				0.784
2				0.209

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	22.24	0.879
2	14.77	0.734
3	6.6	0.335
4	5.48	0.261
5	4.03	0.161

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.

56 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
ANP	4D25	O01378	506.2 Da LogP -2.06 TPSA 281.9	3 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
BEF	3PEW	P20449	66.0 Da LogP 0.88 TPSA 0.0	✓ Ro5	✓ Clean	`[Be-](F)(F)F`
FLQ	2FDC	P56981	516.6 Da LogP 4.09 TPSA 134.2	1 viol.	✓ Clean	`CC(=O)NCCCCCCNC(=O)c1ccc2c(c1)C3(c4ccc(cc4Oc5c3…`
FLU	2NMV	P37954	332.3 Da LogP 3.97 TPSA 87.7	✓ Ro5	✓ Clean	`c1ccc(c(c1)C2=C3C=CC(=O)C=C3Oc4c2ccc(c4)O)C(=O)O`
IHP	3RRN	P20449	660.0 Da LogP -3.13 TPSA 400.6	3 viol.	✓ Clean	`C1(C(C(C(C(C1OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)O…`
M2A	5ELX	P20449	560.4 Da LogP 0.16 TPSA 250.7	3 viol.	✓ Clean	`CNc1ccccc1C(=O)O[C@@H]2[C@@H]([C@@H](O[C@H]2n3c…`

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
ZINC3872582	1.000	332.3 Da LogP 3.97 TPSA 87.7	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1-c1c2ccc(=O)cc-2oc2cc(O)ccc12`
ZINC205587376	0.821	474.5 Da LogP 3.91 TPSA 131.1	✓ Ro5	✓ Clean	`NCCCCCCNC(=O)c1ccc2c(c1)C1(OC2=O)c2ccc(O)cc2Oc2…`
ZINC12360002	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC12360703	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC12503599	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC16546165	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO[P@](=O)(O)OP(=O)(…`
ZINC31977053	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)OP(=O)…`
ZINC4806433	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC53683898	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586019	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)OP(=O)…`
ZINC8586020	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586021	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@@](=O)(O)OP(=O…`
ZINC8586022	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC101257688	0.807	489.5 Da LogP 4.04 TPSA 142.4	✓ Ro5	✓ Clean	`O=C(O)CCCCCNC(=O)c1ccc2c(c1)C1(OC2=O)c2ccc(O)cc…`
ZINC5030658	0.771	376.3 Da LogP 3.67 TPSA 125.0	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2c3ccc(=O)cc-3oc3cc(O)ccc23)c(C(=…`
ZINC4344388	0.760	346.3 Da LogP 4.06 TPSA 76.7	✓ Ro5	✓ Clean	`COC(=O)c1ccccc1-c1c2ccc(=O)cc-2oc2cc(O)ccc12`
ZINC4582277	0.756	304.3 Da LogP 3.98 TPSA 70.7	✓ Ro5	✓ Clean	`O=c1ccc2c(-c3ccccc3O)c3ccc(O)cc3oc-2c1`
ZINC5248684	0.755	376.3 Da LogP 3.67 TPSA 125.0	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)O)c(-c2c3ccc(=O)cc-3oc3cc(O)cc…`
ZINC13518964	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC1532515	0.741	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	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC1842158	0.741	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	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC2126310	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3201891	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC3201893	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3830180	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3860156	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3977897	0.741	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	0.741	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	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC4096224	0.729	346.2 Da LogP -1.90 TPSA 191.9	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](N)(=O)O)[C@@…`
ZINC12503850	0.726	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)OS(=O)…`
ZINC141161066	0.726	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)OS(=O)…`
ZINC141163786	0.726	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)OS(=O)…`
ZINC4228246	0.726	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OS(=O…`
ZINC13556870	0.722	420.1 Da LogP -3.48 TPSA 261.0	1 viol.	✓ Clean	`O=P(O)(O)O[C@H]1[C@@H](O)[C@@H](O)[C@H](O)[C@@H…`
ZINC71789368	0.722	420.1 Da LogP -3.48 TPSA 261.0	1 viol.	✓ Clean	`O=P(O)(O)O[C@H]1[C@H](OP(=O)(O)O)[C@@H](O)[C@H]…`
ZINC71792243	0.722	420.1 Da LogP -3.48 TPSA 261.0	1 viol.	✓ Clean	`O=P(O)(O)O[C@H]1[C@H](O)[C@@H](O)[C@@H](O)[C@@H…`
ZINC205997784	0.721	458.4 Da LogP 4.10 TPSA 153.9	✓ Ro5	Alert	`[N-]=[N+]=NCCCNC(=O)c1ccc2c(c1)C1(OC2=O)c2ccc(O…`
ZINC25762071	0.720	362.3 Da LogP 3.13 TPSA 139.8	✓ Ro5	✓ Clean	`Nc1cc(C(=O)O)c(-c2c3ccc(=O)cc-3oc3cc(O)ccc23)cc…`
ZINC4344383	0.717	288.3 Da LogP 4.27 TPSA 50.4	✓ Ro5	✓ Clean	`O=c1ccc2c(-c3ccccc3)c3ccc(O)cc3oc-2c1`
ZINC105372833	0.712	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@H](O…`
ZINC105372837	0.712	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@H](O…`
ZINC17107643	0.712	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@@H](…`
ZINC204538551	0.712	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@@H](…`
ZINC953075800	0.712	474.5 Da LogP 3.91 TPSA 131.1	✓ Ro5	✓ Clean	`NCCCCCCNC(=O)c1ccc2c(c1)C(=O)OC21c2ccc(O)cc2Oc2…`
ZINC230495868	0.707	413.4 Da LogP 3.03 TPSA 105.1	✓ Ro5	✓ Clean	`C#CCNC(=O)c1ccc2c(c1)C1(OC2=O)c2ccc(O)cc2Oc2cc(…`
ZINC100015959	0.706	420.1 Da LogP -3.48 TPSA 261.0	1 viol.	✓ Clean	`O=P(O)(O)O[C@H]1[C@H](O)[C@@H](OP(=O)(O)O)[C@H]…`
ZINC1501016356	0.706	420.1 Da LogP -3.48 TPSA 261.0	1 viol.	✓ Clean	`O=P(O)(O)OC1C(O)[C@H](OP(=O)(O)O)C(O)[C@H](OP(=…`

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.