Overview
Basic information about this protein and its source genome.
- Accession
- KP13_02293
- Gene
- AHE42864.1 recB
- Status
- annotated
- Amino acids
- 1178
- Structure source
- AlphaFold + ColabFold
Target profile
Computed evidence for target prioritization.
- Human off-target
- No hit
- Human identity (%)
- 0.0
- Gut microbiome off-target
- hit
- Essential (DEG)
- Y
- DEG identity (%)
- 75.424
- DEG E-value
- 0.0
- Localization
- Cytoplasmic
- ColabFold pLDDT
- 90.05
Selected Druggability evidence
AlphaFold / UniProt modelSelected 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.
Sequence
Primary amino-acid sequence viewer.
Functional Annotations
Enzyme classification and Gene Ontology terms linked to this protein.
Gene Ontology (GO)
12- GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
- GO:0003678 Unwinding of a DNA helix, driven by ATP hydrolysis.
- GO:0008854 Catalysis of the exonucleolytic cleavage (in the presence of ATP) in either 5' to 3' or 3' to 5' direction to yield 5'-phosphooligonucleotides.
- 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.
- GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
- GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
- GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
- GO:0009338 An enzyme complex that catalyzes exonucleolytic cleavage (in the presence of ATP) in either 5' to 3' or 3' to 5' direction to yield 5'-phosphooligonucleotides. Exodeoxyribonuclease V shows a preference for double-stranded DNA and possesses DNA-dependent ATPase activity. It acts endonucleolytically on single-stranded circular DNA.
- GO:0043138 Unwinding a DNA helix in the direction 5' to 3', driven by ATP hydrolysis.
- 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:0000287 Binding to a magnesium (Mg) ion.
- GO:0000724 The error-free repair of a double-strand break in DNA in which the broken DNA molecule is repaired using homologous sequences. A strand in the broken DNA searches for a homologous region in an intact chromosome to serve as the template for DNA synthesis. The restoration of two intact DNA molecules results in the exchange, reciprocal or nonreciprocal, of genetic material between the intact DNA molecule and the broken DNA molecule.
Sequence Features
Domain/signature hits from InterPro and related databases.
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 19 | 826 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases |
| 19 | 826 | InterPro | IPR027417 | P-loop containing nucleoside triphosphate hydrolase |
| 480 | 746 | ProSiteProfiles | PS51217 | UvrD-like DNA helicase C-terminal domain profile. |
| 480 | 746 | InterPro | IPR014017 | UvrD-like DNA helicase, C-terminal |
| 886 | 1177 | Gene3D | G3DSA:3.90.320.10 | - |
| 886 | 1177 | InterPro | IPR011604 | PD-(D/E)XK endonuclease-like domain superfamily |
| 2 | 450 | ProSiteProfiles | PS51198 | UvrD-like DNA helicase ATP-binding domain profile. |
| 2 | 450 | InterPro | IPR014016 | UvrD-like helicase, ATP-binding domain |
| 947 | 1140 | Pfam | PF12705 | PD-(D/E)XK nuclease superfamily |
| 947 | 1140 | InterPro | IPR038726 | PD-(D/E)XK endonuclease-like domain, AddAB-type |
| 8 | 1169 | NCBIfam | TIGR00609 | exodeoxyribonuclease V subunit beta |
| 8 | 1169 | InterPro | IPR004586 | RecBCD enzyme subunit RecB |
| 898 | 1166 | CDD | cd22352 | RecB_C-like |
| 15 | 436 | Pfam | PF00580 | UvrD/REP helicase N-terminal domain |
| 15 | 436 | InterPro | IPR014016 | UvrD-like helicase, ATP-binding domain |
| 215 | 235 | Coils | Coil | Coil |
| 886 | 1176 | FunFam | G3DSA:3.90.320.10:FF:000003 | RecBCD enzyme subunit RecB |
| 8 | 436 | Gene3D | G3DSA:3.40.50.300 | - |
| 8 | 436 | InterPro | IPR027417 | P-loop containing nucleoside triphosphate hydrolase |
| 896 | 1171 | SUPERFAMILY | SSF52980 | Restriction endonuclease-like |
| 896 | 1171 | InterPro | IPR011335 | Restriction endonuclease type II-like |
| 736 | 816 | CDD | cd18807 | SF1_C_UvrD |
| 5 | 1170 | Hamap | MF_01485 | RecBCD enzyme subunit RecB [recB]. |
| 5 | 1170 | InterPro | IPR004586 | RecBCD enzyme subunit RecB |
| 19 | 833 | PANTHER | PTHR11070 | UVRD / RECB / PCRA DNA HELICASE FAMILY MEMBER |
| 19 | 833 | InterPro | IPR000212 | DNA helicase, UvrD/REP type |
| 583 | 728 | Gene3D | G3DSA:1.10.486.10 | PCRA; domain 4 |
| 445 | 843 | Gene3D | G3DSA:3.40.50.300 | - |
| 445 | 843 | InterPro | IPR027417 | P-loop containing nucleoside triphosphate hydrolase |
| 782 | 809 | Coils | Coil | Coil |
| 155 | 349 | Gene3D | G3DSA:1.10.3170.10 | Recbcd, chain B, domain 2 |
| 441 | 809 | Pfam | PF13361 | UvrD-like helicase C-terminal domain |
| 441 | 809 | InterPro | IPR014017 | UvrD-like DNA helicase, C-terminal |
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...
Structural evidence
0 + 2Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.
| Entry | Method | Resolution | Chain | Coverage | Links | Status |
|---|---|---|---|---|---|---|
|
AlphaFold
AF_A0A0H3GSM0
|
AlphaFold | — | — | full sequence | — | Viewing |
|
ColabFold
KP13_02293
|
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 |
|---|---|---|---|---|---|---|---|
| 5 | 0.499 |
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 | 13.9 | 0.703 | ||||||
| 2 | 12.49 | 0.653 | ||||||
| 3 | 8.77 | 0.469 | ||||||
| 4 | 5.34 | 0.253 | ||||||
| 5 | 5.06 | 0.231 |
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 |
|---|---|---|---|---|---|---|---|
| 100 | 0.227 |
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 | 13.83 | 0.701 | ||||||
| 2 | 13.11 | 0.674 | ||||||
| 3 | 9.63 | 0.518 | ||||||
| 4 | 4.94 | 0.223 | ||||||
| 5 | 3.93 | 0.155 |
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.
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.
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 |
|---|---|---|---|---|---|
| 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(=…
|
| 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…
|
| 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](…
|
| ZINC31475423 | 0.703 | 434.3 Da LogP -2.99 TPSA 238.4 | 2 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@H]1O[C@H](CO[P@@](=O)(O)OC(=O)…
|
| ZINC105469665 | 0.694 | 425.2 Da LogP -1.64 TPSA 223.4 | 2 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)CP(=O…
|
| ZINC13527614 | 0.694 | 425.2 Da LogP -1.64 TPSA 223.4 | 2 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)CP(=O)…
|
| ZINC219330894 | 0.694 | 425.2 Da LogP -1.64 TPSA 223.4 | 2 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)CP(=O)…
|
| ZINC3873852 | 0.694 | 425.2 Da LogP -1.64 TPSA 223.4 | 2 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)CP(=O)…
|
| ZINC3873853 | 0.694 | 425.2 Da LogP -1.64 TPSA 223.4 | 2 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@](=O)(O)CP(=O…
|
| ZINC3873854 | 0.694 | 425.2 Da LogP -1.64 TPSA 223.4 | 2 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)CP(=O)…
|
| ZINC3873855 | 0.694 | 425.2 Da LogP -1.64 TPSA 223.4 | 2 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@](=O)(O)CP(=O…
|
| ZINC5615251 | 0.677 | 375.3 Da LogP -0.55 TPSA 164.1 | 1 viol. | ✓ Clean |
COP(=O)(OC)OC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@…
|
| ZINC5615253 | 0.677 | 375.3 Da LogP -0.55 TPSA 164.1 | 1 viol. | ✓ Clean |
COP(=O)(OC)OC[C@@H]1O[C@@H](n2cnc3c(N)ncnc32)[C…
|
| ZINC5615258 | 0.677 | 375.3 Da LogP -0.55 TPSA 164.1 | 1 viol. | ✓ Clean |
COP(=O)(OC)OC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@…
|
| ZINC5615263 | 0.677 | 375.3 Da LogP -0.55 TPSA 164.1 | 1 viol. | ✓ Clean |
COP(=O)(OC)OC[C@@H]1O[C@@H](n2cnc3c(N)ncnc32)[C…
|
| ZINC31516918 | 0.672 | 446.4 Da LogP -1.33 TPSA 218.2 | 1 viol. | ✓ Clean |
CC(C)[C@H](N)C(=O)O[P@](=O)(O)OC[C@H]1O[C@@H](n…
|
| ZINC1582675 | 0.667 | 403.3 Da LogP 0.23 TPSA 164.1 | 1 viol. | ✓ Clean |
CCOP(=O)(OCC)OC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[…
|
| ZINC5486730 | 0.667 | 403.3 Da LogP 0.23 TPSA 164.1 | 1 viol. | ✓ Clean |
CCOP(=O)(OCC)OC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[…
|
| ZINC5486734 | 0.667 | 403.3 Da LogP 0.23 TPSA 164.1 | 1 viol. | ✓ Clean |
CCOP(=O)(OCC)OC[C@@H]1O[C@@H](n2cnc3c(N)ncnc32)…
|
| ZINC5486740 | 0.667 | 403.3 Da LogP 0.23 TPSA 164.1 | 1 viol. | ✓ Clean |
CCOP(=O)(OCC)OC[C@@H]1O[C@@H](n2cnc3c(N)ncnc32)…
|
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.