Overview
Basic information about this protein and its source genome.
- Accession
- PA1843
- Gene
- PA1843 metH
- Status
- annotated
- Amino acids
- 1234
- Structure source
- AlphaFold
Target profile
Computed evidence for target prioritization.
- Human off-target
- hit
- Human identity (%)
- 57.806
- Human E-value
- 1.34e-83
- Gut microbiome off-target
- hit
- Essential (DEG)
- N
- 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.
Sequence
Primary amino-acid sequence viewer.
Functional Annotations
Enzyme classification and Gene Ontology terms linked to this protein.
Enzyme Commission (EC)
1Gene Ontology (GO)
11- GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
- GO:0031419 Binding to cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom.
- GO:0008705 Catalysis of the reaction: (6S)-5-methyl-5,6,7,8-tetrahydrofolate + L-homocysteine = (6S)-5,6,7,8-tetrahydrofolate + L-methionine.
- GO:0008270 Binding to a zinc ion (Zn).
- GO:0050667 The chemical reactions and pathways involving homocysteine, the amino acid alpha-amino-gamma-mercaptobutanoic acid. Homocysteine is an important intermediate in the metabolic reactions of its S-methyl derivative, methionine.
- GO:0009086 OBSOLETE. The chemical reactions and pathways resulting in the de novo formation of L-methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins.
- GO:0032259 The process in which a methyl group is covalently attached to a molecule.
- GO:0046653 The chemical reactions and pathways involving tetrahydrofolate, 5,6,7,8-tetrahydrofolic acid, a folate derivative bearing additional hydrogens on the pterin group.
- GO:0046872 Binding to a metal ion.
- GO:0042558 The chemical reactions and pathways involving any compound containing pteridine (pyrazino(2,3-dipyrimidine)), e.g. pteroic acid, xanthopterin and folic acid.
- GO:0044237 OBSOLETE. The chemical reactions and pathways by which individual cells transform chemical substances.
Sequence Features
Domain/signature hits from InterPro and related databases.
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 664 | 878 | CDD | cd02069 | methionine_synthase_B12_BD |
| 664 | 878 | InterPro | IPR033706 | Methionine synthase, B12-binding domain |
| 904 | 1234 | ProSiteProfiles | PS50974 | AdoMet activation domain profile. |
| 904 | 1234 | InterPro | IPR004223 | Vitamin B12-dependent methionine synthase, activation domain |
| 20 | 1200 | NCBIfam | TIGR02082 | methionine synthase |
| 20 | 1200 | InterPro | IPR011822 | Cobalamin-dependent methionine synthase |
| 367 | 605 | Pfam | PF00809 | Pterin binding enzyme |
| 367 | 605 | InterPro | IPR000489 | Pterin-binding domain |
| 664 | 737 | Pfam | PF02607 | B12 binding domain |
| 664 | 737 | InterPro | IPR003759 | Cobalamin (vitamin B12)-binding module, cap domain |
| 9 | 345 | FunFam | G3DSA:3.20.20.330:FF:000001 | Methionine synthase |
| 363 | 619 | CDD | cd00740 | MeTr |
| 750 | 902 | FunFam | G3DSA:3.40.50.280:FF:000001 | Methionine synthase |
| 651 | 745 | Gene3D | G3DSA:1.10.1240.10 | Methionine synthase domain |
| 651 | 745 | InterPro | IPR036594 | Methionine synthase domain |
| 750 | 902 | Gene3D | G3DSA:3.40.50.280 | - |
| 944 | 1101 | Gene3D | G3DSA:1.10.288.10 | - |
| 363 | 624 | ProSiteProfiles | PS50972 | Pterin-binding domain profile. |
| 363 | 624 | InterPro | IPR000489 | Pterin-binding domain |
| 24 | 332 | Pfam | PF02574 | Homocysteine S-methyltransferase |
| 24 | 332 | InterPro | IPR003726 | Homocysteine-binding domain |
| 912 | 1232 | Gene3D | G3DSA:3.10.196.10 | - |
| 912 | 1232 | InterPro | IPR037010 | Vitamin B12-dependent methionine synthase, activation domain superfamily |
| 945 | 1216 | Pfam | PF02965 | Vitamin B12 dependent methionine synthase, activation domain |
| 945 | 1216 | InterPro | IPR004223 | Vitamin B12-dependent methionine synthase, activation domain |
| 752 | 888 | ProSiteProfiles | PS51332 | B12-binding domain profile. |
| 752 | 888 | InterPro | IPR006158 | Cobalamin (vitamin B12)-binding domain |
| 909 | 1233 | SUPERFAMILY | SSF56507 | Methionine synthase activation domain-like |
| 909 | 1233 | InterPro | IPR037010 | Vitamin B12-dependent methionine synthase, activation domain superfamily |
| 9 | 345 | Gene3D | G3DSA:3.20.20.330 | - |
| 9 | 345 | InterPro | IPR036589 | Homocysteine-binding domain superfamily |
| 655 | 749 | ProSiteProfiles | PS51337 | B12-binding N-terminal domain profile. |
| 655 | 749 | InterPro | IPR003759 | Cobalamin (vitamin B12)-binding module, cap domain |
| 754 | 847 | Pfam | PF02310 | B12 binding domain |
| 754 | 847 | InterPro | IPR006158 | Cobalamin (vitamin B12)-binding domain |
| 657 | 744 | SUPERFAMILY | SSF47644 | Methionine synthase domain |
| 657 | 744 | InterPro | IPR036594 | Methionine synthase domain |
| 662 | 745 | SMART | SM01018 | B12_binding_2_2 |
| 662 | 745 | InterPro | IPR003759 | Cobalamin (vitamin B12)-binding module, cap domain |
| 363 | 636 | SUPERFAMILY | SSF51717 | Dihydropteroate synthetase-like |
| 363 | 636 | InterPro | IPR011005 | Dihydropteroate synthase-like |
| 8 | 1203 | PIRSF | PIRSF000381 | Met_synth_MetH |
| 8 | 1203 | InterPro | IPR011822 | Cobalamin-dependent methionine synthase |
| 353 | 650 | Gene3D | G3DSA:3.20.20.20 | - |
| 353 | 650 | InterPro | IPR011005 | Dihydropteroate synthase-like |
| 748 | 900 | SUPERFAMILY | SSF52242 | Cobalamin (vitamin B12)-binding domain |
| 748 | 900 | InterPro | IPR036724 | Cobalamin-binding domain superfamily |
| 651 | 745 | FunFam | G3DSA:1.10.1240.10:FF:000001 | Methionine synthase |
| 12 | 332 | ProSiteProfiles | PS50970 | Homocysteine-binding domain profile. |
| 12 | 332 | InterPro | IPR003726 | Homocysteine-binding domain |
| 13 | 1232 | PANTHER | PTHR45833 | METHIONINE SYNTHASE |
| 15 | 406 | SUPERFAMILY | SSF82282 | Homocysteine S-methyltransferase |
| 15 | 406 | InterPro | IPR036589 | Homocysteine-binding domain superfamily |
| 353 | 649 | FunFam | G3DSA:3.20.20.20:FF:000002 | Methionine synthase |
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 + 1Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.
| Entry | Method | Resolution | Chain | Coverage | Links | Status |
|---|---|---|---|---|---|---|
|
AlphaFold
PA1843
|
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 |
|---|---|---|---|---|---|---|---|
| 1 | 0.431 | ||||||
| 5 | 0.396 | ||||||
| 3 | 0.247 |
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.
| Ligand | Source crystal | UniProt (homolog) | MW · LogP · TPSA | Lipinski | PAINS | SMILES |
|---|---|---|---|---|---|---|
| C2F | Q5SKM5 | 459.5 Da LogP -0.26 TPSA 202.8 | 1 viol. | ✓ Clean |
C[N@@]1[C@H](CNC2=C1C(=O)NC(=N2)N)CNc3ccc(cc3)C…
|
|
| COB | P13009 | — | — | — |
Cc1cc2c(cc1C)n(cn2)[C@@H]3[C@@H]([C@@H]([C@H](O…
|
|
| FLC | Q5SKM5 | 189.1 Da LogP -5.25 TPSA 140.6 | ✓ Ro5 | ✓ Clean |
C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O
|
|
| HCS | Q9WYA5 | 135.2 Da LogP -0.28 TPSA 63.3 | ✓ Ro5 | ✓ Clean |
C(CS)[C@@H](C(=O)O)N
|
|
| SFG | P13009 | 381.4 Da LogP -2.06 TPSA 208.7 | 2 viol. | ✓ Clean |
c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
|
|
| THG | Q99707 | 445.4 Da LogP -0.28 TPSA 211.6 | 1 viol. | ✓ Clean |
c1cc(ccc1C(=O)N[C@@H](CCC(=O)O)C(=O)O)NC[C@H]2C…
|
|
| YT3 | Q9WYA5 | 88.9 Da LogP -0.00 TPSA 0.0 | ✓ Ro5 | ✓ Clean |
[Y+3]
|
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 |
|---|---|---|---|---|---|
| ZINC13650200 | 1.000 | 381.4 Da LogP -2.06 TPSA 208.6 | 2 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@H](C[C@H](N)CC[C@H](N)…
|
| ZINC2005305 | 1.000 | 459.5 Da LogP -0.26 TPSA 202.8 | 1 viol. | ✓ Clean |
CN1c2c(nc(N)[nH]c2=O)NC[C@@H]1CNc1ccc(C(=O)N[C@…
|
| ZINC205994753 | 1.000 | 381.4 Da LogP -2.06 TPSA 208.6 | 2 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@H](C[C@H](N)CC[C@H](N)…
|
| ZINC205994774 | 1.000 | 381.4 Da LogP -2.06 TPSA 208.6 | 2 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@H](C[C@H](N)CC[C@H](N)…
|
| ZINC2572666 | 1.000 | 459.5 Da LogP -0.26 TPSA 202.8 | 1 viol. | ✓ Clean |
CN1c2c(nc(N)[nH]c2=O)NC[C@H]1CNc1ccc(C(=O)N[C@@…
|
| ZINC27723577 | 1.000 | 381.4 Da LogP -2.06 TPSA 208.6 | 2 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@H](C[C@H](N)CC[C@H](N)…
|
| ZINC38192471 | 1.000 | 381.4 Da LogP -2.06 TPSA 208.6 | 2 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@H](C[C@H](N)CC[C@@H](N…
|
| ZINC38192472 | 1.000 | 381.4 Da LogP -2.06 TPSA 208.6 | 2 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@H](C[C@@H](N)CC[C@@H](…
|
| ZINC4217451 | 1.000 | 381.4 Da LogP -2.06 TPSA 208.6 | 2 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@H](C[C@@H](N)CC[C@H](N…
|
| ZINC4228266 | 1.000 | 459.5 Da LogP -0.26 TPSA 202.8 | 1 viol. | ✓ Clean |
CN1c2c(nc(N)[nH]c2=O)NC[C@@H]1CNc1ccc(C(=O)N[C@…
|
| ZINC4228267 | 1.000 | 459.5 Da LogP -0.26 TPSA 202.8 | 1 viol. | ✓ Clean |
CN1c2c(nc(N)[nH]c2=O)NC[C@H]1CNc1ccc(C(=O)N[C@H…
|
| ZINC9212425 | 0.803 | 473.4 Da LogP -0.73 TPSA 219.8 | 1 viol. | ✓ Clean |
Nc1nc2c(c(=O)[nH]1)N(C=O)[C@@H](CNc1ccc(C(=O)N[…
|
| ZINC9212426 | 0.803 | 473.4 Da LogP -0.73 TPSA 219.8 | 1 viol. | ✓ Clean |
Nc1nc2c(c(=O)[nH]1)N(C=O)[C@H](CNc1ccc(C(=O)N[C…
|
| ZINC9212427 | 0.803 | 473.4 Da LogP -0.73 TPSA 219.8 | 1 viol. | ✓ Clean |
Nc1nc2c(c(=O)[nH]1)N(C=O)[C@@H](CNc1ccc(C(=O)N[…
|
| ZINC9212428 | 0.803 | 473.4 Da LogP -0.73 TPSA 219.8 | 1 viol. | ✓ Clean |
Nc1nc2c(c(=O)[nH]1)N(C=O)[C@H](CNc1ccc(C(=O)N[C…
|
| ZINC13522400 | 0.737 | 400.4 Da LogP -2.42 TPSA 199.7 | 1 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@H](C[S@](=O)CC[C@H](N)…
|
| ZINC13522403 | 0.737 | 400.4 Da LogP -2.42 TPSA 199.7 | 1 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@H](C[S@@](=O)CC[C@H](N…
|
| ZINC13522378 | 0.732 | 370.4 Da LogP -1.83 TPSA 182.6 | 1 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@H](CSC[C@H](N)C(=O)O)[…
|
| ZINC13522407 | 0.732 | 370.4 Da LogP -1.83 TPSA 182.6 | 1 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@H](CSC[C@H](N)C(=O)O)[…
|
| ZINC256828117 | 0.732 | 370.4 Da LogP -1.83 TPSA 182.6 | 1 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@H](CSC[C@H](N)C(=O)O)[…
|
| ZINC256828118 | 0.732 | 370.4 Da LogP -1.83 TPSA 182.6 | 1 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@H](CSC[C@H](N)C(=O)O)[…
|
| ZINC1775937521 | 0.726 | 423.5 Da LogP -1.02 TPSA 194.7 | 2 viol. | ✓ Clean |
CCCN[C@H](CC[C@H](N)C(=O)O)C[C@H]1O[C@@H](n2cnc…
|
| ZINC95921230 | 0.726 | 423.5 Da LogP -1.02 TPSA 194.7 | 2 viol. | ✓ Clean |
CCCN[C@@H](CC[C@H](N)C(=O)O)C[C@H]1O[C@@H](n2cn…
|
| ZINC12501055 | 0.724 | 384.4 Da LogP -1.44 TPSA 182.6 | 1 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@H](CSCC[C@H](N)C(=O)O)…
|
| ZINC13509082 | 0.724 | 384.4 Da LogP -1.44 TPSA 182.6 | 1 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@H]1O[C@@H](CSCC[C@@H](N)C(=O)O…
|
| ZINC13509104 | 0.724 | 384.4 Da LogP -1.44 TPSA 182.6 | 1 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@H](CSCC[C@@H](N)C(=O)O…
|
| ZINC1532516 | 0.724 | 384.4 Da LogP -1.44 TPSA 182.6 | 1 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@H]1O[C@@H](CSCC[C@H](N)C(=O)O)…
|
| ZINC33821012 | 0.724 | 384.4 Da LogP -1.44 TPSA 182.6 | 1 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@H](CSCC[C@H](N)C(=O)O)…
|
| ZINC33821013 | 0.724 | 384.4 Da LogP -1.44 TPSA 182.6 | 1 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@H](CSCC[C@H](N)C(=O)O)…
|
| ZINC4228232 | 0.724 | 384.4 Da LogP -1.44 TPSA 182.6 | 1 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@H](CSCC[C@H](N)C(=O)O)…
|
| ZINC45789230 | 0.724 | 384.4 Da LogP -1.44 TPSA 182.6 | 1 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CSCC[C@H](N)C(=O)O…
|
| ZINC45789233 | 0.724 | 384.4 Da LogP -1.44 TPSA 182.6 | 1 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@H]1O[C@H](CSCC[C@H](N)C(=O)O)[…
|
| ZINC49014951 | 0.724 | 416.4 Da LogP -2.76 TPSA 216.8 | 1 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@H]1O[C@H](CS(=O)(=O)CC[C@H](N)…
|
| ZINC49014955 | 0.724 | 416.4 Da LogP -2.76 TPSA 216.8 | 1 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@H]1O[C@H](CS(=O)(=O)CC[C@@H](N…
|
| ZINC100005972 | 0.712 | 400.5 Da LogP -1.54 TPSA 182.6 | 1 viol. | ✓ Clean |
C[S@@H](CC[C@H](N)C(=O)O)C[C@H]1O[C@@H](n2cnc3c…
|
| ZINC8655682 | 0.711 | 487.5 Da LogP -0.34 TPSA 219.8 | 1 viol. | ✓ Clean |
Nc1nc2c(c(=O)[nH]1)N(C=O)[C@@H](CCNc1ccc(C(=O)N…
|
| ZINC4228235 | 0.708 | 445.4 Da LogP -0.28 TPSA 211.6 | 1 viol. | ✓ Clean |
Nc1nc2c(c(=O)[nH]1)N[C@H](CNc1ccc(C(=O)N[C@@H](…
|
| ZINC4228236 | 0.708 | 445.4 Da LogP -0.28 TPSA 211.6 | 1 viol. | ✓ Clean |
Nc1nc2c(c(=O)[nH]1)N[C@H](CNc1ccc(C(=O)N[C@H](C…
|
| ZINC4228237 | 0.708 | 445.4 Da LogP -0.28 TPSA 211.6 | 1 viol. | ✓ Clean |
Nc1nc2c(c(=O)[nH]1)N[C@@H](CNc1ccc(C(=O)N[C@@H]…
|
| ZINC4228238 | 0.708 | 445.4 Da LogP -0.28 TPSA 211.6 | 1 viol. | ✓ Clean |
Nc1nc2c(c(=O)[nH]1)N[C@@H](CNc1ccc(C(=O)N[C@H](…
|
| ZINC12371977 | 0.700 | 399.5 Da LogP -1.92 TPSA 182.6 | ✓ Ro5 | ✓ Clean |
C[S@@+](CC[C@H](N)C(=O)O)C[C@H]1O[C@@H](n2cnc3c…
|
| ZINC12371978 | 0.700 | 399.5 Da LogP -1.92 TPSA 182.6 | ✓ Ro5 | ✓ Clean |
C[S@+](CC[C@H](N)C(=O)O)C[C@H]1O[C@@H](n2cnc3c(…
|
| ZINC13522357 | 0.700 | 399.5 Da LogP -1.92 TPSA 182.6 | ✓ Ro5 | ✓ Clean |
C[S@@+](CC[C@@H](N)C(=O)O)C[C@H]1O[C@@H](n2cnc3…
|
| ZINC13522362 | 0.700 | 399.5 Da LogP -1.92 TPSA 182.6 | ✓ Ro5 | ✓ Clean |
C[S@+](CC[C@@H](N)C(=O)O)C[C@H]1O[C@@H](n2cnc3c…
|
| ZINC254297245 | 0.700 | 399.5 Da LogP -1.92 TPSA 182.6 | ✓ Ro5 | ✓ Clean |
C[S@+](CC[C@H](N)C(=O)O)C[C@@H]1O[C@H](n2cnc3c(…
|
| ZINC254297257 | 0.700 | 399.5 Da LogP -1.92 TPSA 182.6 | ✓ Ro5 | ✓ Clean |
C[S@+](CC[C@H](N)C(=O)O)C[C@@H]1O[C@H](n2cnc3c(…
|
| ZINC4214738 | 0.700 | 399.5 Da LogP -1.92 TPSA 182.6 | ✓ Ro5 | ✓ Clean |
C[S@@+](CC[C@H](N)C(=O)O)C[C@H]1O[C@@H](n2cnc3c…
|
| ZINC71755557 | 0.700 | 399.5 Da LogP -1.92 TPSA 182.6 | ✓ Ro5 | ✓ Clean |
C[S@@+](CC[C@@H](N)C(=O)O)C[C@@H]1O[C@H](n2cnc3…
|
| ZINC95644663 | 0.700 | 399.5 Da LogP -1.92 TPSA 182.6 | ✓ Ro5 | ✓ Clean |
C[S@@+](CC[C@H](N)C(=O)O)C[C@H]1O[C@@H](n2cnc3c…
|
| ZINC95644664 | 0.700 | 399.5 Da LogP -1.92 TPSA 182.6 | ✓ Ro5 | ✓ Clean |
C[S@+](CC[C@H](N)C(=O)O)C[C@H]1O[C@@H](n2cnc3c(…
|
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.