Cavities are compared using Shaper.
For more information, please see the following publication:
Desaphy J. et al. Comparison and Druggability Prediction of protein-Ligand Binding sites from pharmacophore-annotated cavity shapes J. Chem. Inf. Model., 2012, 52(8), pp2287-2299
PDB ID | HET | Uniprot Name | EC Number |
---|---|---|---|
3nl1 | GTQ | Gentisate 1,2-dioxygenase |
PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
---|---|---|---|---|---|
3nl1 | GTQ | Gentisate 1,2-dioxygenase | / | 1.000 | |
3nw4 | GTQ | Gentisate 1,2-dioxygenase | / | 0.673 | |
3nkt | 1HN | Gentisate 1,2-dioxygenase | / | 0.644 | |
4fag | GTQ | Gentisate 1,2-dioxygenase | / | 0.529 | |
3c14 | FOK | Adenylate cyclase type 2 | / | 0.509 | |
3c14 | FOK | Adenylate cyclase type 5 | / | 0.509 | |
4lga | A2O | Abscisic acid receptor PYL2 | / | 0.496 | |
3nxr | D2D | Dihydrofolate reductase | 1.5.1.3 | 0.493 | |
3kb0 | A8S | Abscisic acid receptor PYL2 | / | 0.491 | |
1w78 | PD8 | Dihydrofolate synthase/folylpolyglutamate synthase | 6.3.2.12 | 0.487 | |
1m2x | MCO | Metallo-beta-lactamase type 2 | / | 0.486 | |
2v58 | LZJ | Biotin carboxylase | 6.3.4.14 | 0.486 | |
3hxc | BD6 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.485 | |
1opb | RET | Retinol-binding protein 2 | / | 0.484 | |
4emy | PLP | Aminotransferase class I and II | / | 0.482 | |
3tr9 | PT1 | Dihydropteroate synthase | / | 0.480 | |
4c9w | VGH | 7,8-dihydro-8-oxoguanine triphosphatase | 3.6.1.55 | 0.480 | |
1j3k | WRA | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.477 | |
1ly4 | COQ | Dihydrofolate reductase | 1.5.1.3 | 0.477 | |
1mlz | PLP | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase | 2.6.1.62 | 0.477 | |
1qy2 | IPZ | Major urinary protein 1 | / | 0.476 | |
1dr4 | HBI | Dihydrofolate reductase | 1.5.1.3 | 0.475 | |
3pn1 | IVH | DNA ligase | / | 0.475 | |
3nxv | D2F | Dihydrofolate reductase | 1.5.1.3 | 0.474 | |
1cjv | FOK | Adenylate cyclase type 2 | / | 0.473 | |
1cjv | FOK | Adenylate cyclase type 5 | / | 0.473 | |
3zku | HCV | Isopenicillin N synthase | 1.21.3.1 | 0.473 | |
1ddt | APU | Diphtheria toxin | / | 0.472 | |
2our | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.472 | |
4dpd | DHF | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.472 | |
1xor | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.471 | |
2bfm | TOP | Pteridine reductase 1 | 1.5.1.33 | 0.471 | |
3ghv | GHC | Dihydrofolate reductase | 1.5.1.3 | 0.471 | |
3zvu | A8S | Abscisic acid receptor PYR1 | / | 0.470 | |
4jda | A9S | Abscisic acid receptor PYL3 | / | 0.470 | |
1soj | IBM | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.469 | |
3ntz | 3TZ | Dihydrofolate reductase | 1.5.1.3 | 0.469 | |
3sni | 546 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.469 | |
1mvs | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.468 | |
1xj7 | DHT | Androgen receptor | / | 0.467 | |
3k3k | A8S | Abscisic acid receptor PYR1 | / | 0.467 | |
1cs4 | FOK | Adenylate cyclase type 2 | / | 0.466 | |
1cs4 | FOK | Adenylate cyclase type 5 | / | 0.466 | |
1cjt | FOK | Adenylate cyclase type 2 | / | 0.465 | |
1cjt | FOK | Adenylate cyclase type 5 | / | 0.465 | |
1mvc | BM6 | Retinoic acid receptor RXR-alpha | / | 0.465 | |
2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.465 | |
3kdi | A8S | Abscisic acid receptor PYL2 | / | 0.465 | |
3nxy | D2H | Dihydrofolate reductase | 1.5.1.3 | 0.465 | |
4kfj | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.465 | |
4mv3 | ACP | Biotin carboxylase | 6.3.4.14 | 0.465 | |
1pd8 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.464 | |
3kb3 | A8S | Abscisic acid receptor PYL2 | / | 0.464 | |
3pd4 | A3G | Threonine--tRNA ligase | 6.1.1.3 | 0.463 | |
3sa2 | 7DR | Dihydrofolate reductase | / | 0.462 | |
3zrb | OR8 | Progesterone receptor | / | 0.462 | |
1tl7 | FOK | Adenylate cyclase type 2 | / | 0.461 | |
1tl7 | FOK | Adenylate cyclase type 5 | / | 0.461 | |
2od7 | A1R | NAD-dependent protein deacetylase HST2 | 3.5.1 | 0.461 | |
2vqs | BVD | Deoxynucleoside kinase | / | 0.461 | |
4juf | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.461 | |
4n1g | CEI | Obelin | / | 0.461 | |
1crb | RTL | Retinol-binding protein 1 | / | 0.460 | |
4kak | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
4mv1 | ADP | Biotin carboxylase | 6.3.4.14 | 0.460 | |
2q7o | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.459 | |
3hxe | BD8 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.459 | |
3q9b | B3N | Acetylpolyamine amidohydrolase | / | 0.459 | |
1tg2 | H2B | Phenylalanine-4-hydroxylase | 1.14.16.1 | 0.458 | |
2ipj | FFA | Aldo-keto reductase family 1 member C2 | / | 0.458 | |
4m6l | 21V | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
5kf1 | ACO | Predicted acetyltransferase | / | 0.458 | |
1sr7 | MOF | Progesterone receptor | / | 0.457 | |
2fzi | DH3 | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
2gvd | FKP | Adenylate cyclase type 2 | / | 0.457 | |
2gvd | FKP | Adenylate cyclase type 5 | / | 0.457 | |
3hxd | BD7 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.457 | |
3jun | AKD | Phenazine biosynthesis protein A/B | / | 0.456 | |
3r33 | 6ME | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
4jq2 | SUZ | Aldo-keto reductase family 1 member C2 | / | 0.456 | |
5h8t | RTL | Retinol-binding protein 1 | / | 0.456 | |
1wxy | FRK | Adenosine deaminase | 3.5.4.4 | 0.455 | |
2ada | HPR | Adenosine deaminase | 3.5.4.4 | 0.455 | |
2cfc | KPC | 2-(R)-hydroxypropyl-CoM dehydrogenase | 1.1.1.268 | 0.455 | |
2fzj | DH3 | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
2p1u | 4TN | Retinoic acid receptor RXR-alpha | / | 0.455 | |
2vcz | VC3 | Hematopoietic prostaglandin D synthase | / | 0.455 | |
3ujl | A8S | Abscisic acid receptor PYL2 | / | 0.455 | |
4hfn | CIY | 2-alkenal reductase (NADP(+)-dependent) | / | 0.455 | |
4jlt | 8PR | Cytochrome P450 2B4 | 1.14.14.1 | 0.455 | |
4l7v | SAH | Protein-L-isoaspartate O-methyltransferase | / | 0.455 | |
1trg | CB3 | Thymidylate synthase | / | 0.454 | |
1zrb | 062 | Prothrombin | 3.4.21.5 | 0.454 | |
2v3h | I25 | Prothrombin | 3.4.21.5 | 0.454 | |
3qpg | 3QP | Aspartate aminotransferase | 2.6.1.1 | 0.454 | |
4kko | 1RE | Gag-Pol polyprotein | 2.7.7.49 | 0.454 | |
4l1x | STR | Aldo-keto reductase family 1 member C2 | / | 0.454 | |
1ihi | IU5 | Aldo-keto reductase family 1 member C2 | / | 0.453 | |
1syn | F89 | Thymidylate synthase | / | 0.453 | |
3lal | KRV | Gag-Pol polyprotein | 2.7.7.49 | 0.453 | |
3qlx | QLR | Uncharacterized protein | / | 0.453 | |
4zn7 | DES | Estrogen receptor | / | 0.453 | |
1cul | FOK | Adenylate cyclase type 2 | / | 0.452 | |
1cul | FOK | Adenylate cyclase type 5 | / | 0.452 | |
1xon | PIL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.452 | |
2jc6 | QPP | Calcium/calmodulin-dependent protein kinase type 1D | 2.7.11.17 | 0.452 | |
2pix | DHT | Androgen receptor | / | 0.452 | |
2uag | UMA | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.452 | |
3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
3vg9 | ZMA | Adenosine receptor A2a | / | 0.452 | |
4jbx | SK7 | Thymidine kinase | / | 0.452 | |
5ai5 | BSU | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.452 | |
1e3k | R18 | Progesterone receptor | / | 0.451 | |
2w6o | OA3 | Biotin carboxylase | 6.3.4.14 | 0.451 | |
2w71 | L23 | Biotin carboxylase | 6.3.4.14 | 0.451 | |
3zec | ANP | Adenosine monophosphate-protein transferase SoFic | 2.7.7.n1 | 0.451 | |
4jvl | EST | Estrogen sulfotransferase | 2.8.2.4 | 0.451 | |
4jxz | ATP | Glutamine--tRNA ligase | 6.1.1.18 | 0.451 | |
1x2h | LPA | Lipoate-protein ligase A | 6.3.1.20 | 0.450 | |
3d75 | NBB | Pheromone-binding protein ASP1 | / | 0.450 | |
3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.450 | |
3k47 | D09 | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
3k4s | 0MO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.450 | |
3kdj | A8S | Abscisic acid receptor PYL1 | / | 0.450 | |
3p8i | FMN | Pentaerythritol tetranitrate reductase | / | 0.450 | |
3tyd | XHP | Dihydropteroate synthase | / | 0.450 | |
4g8c | C6L | Alpha/beta hydrolase fold protein | / | 0.450 | |
1al7 | HST | Peroxisomal (S)-2-hydroxy-acid oxidase | 1.1.3.15 | 0.449 | |
1dhi | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
1kms | LIH | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
1y2e | 5DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.449 | |
1y56 | FMN | Uncharacterized protein | / | 0.449 | |
1y56 | FMN | 382aa long hypothetical sarcosine oxidase | / | 0.449 | |
2o8h | 227 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.449 | |
2pdf | ZST | Aldose reductase | 1.1.1.21 | 0.449 | |
2yat | EEU | Estrogen receptor | / | 0.449 | |
3erd | DES | Estrogen receptor | / | 0.449 | |
3zrb | ORC | Progesterone receptor | / | 0.449 | |
4jq4 | IMN | Aldo-keto reductase family 1 member C2 | / | 0.449 | |
1cjk | FOK | Adenylate cyclase type 2 | / | 0.448 | |
1cjk | FOK | Adenylate cyclase type 5 | / | 0.448 | |
1klk | PMD | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
1mvt | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
1rx5 | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
2bbq | PFG | Thymidylate synthase | / | 0.448 | |
2iej | S48 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.448 | |
2ov2 | GCP | Ras-related C3 botulinum toxin substrate 3 | / | 0.448 | |
3i1y | 33N | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.448 | |
1s3y | TQT | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
2fzh | DH1 | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
2ix5 | CAA | Acyl-coenzyme A oxidase 4, peroxisomal | 1.3.3.6 | 0.447 | |
2v3w | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.447 | |
2vdy | HCY | Corticosteroid-binding globulin | / | 0.447 | |
3nj0 | PYV | Abscisic acid receptor PYL2 | / | 0.447 | |
3o9p | MHI | Periplasmic murein peptide-binding protein | / | 0.447 | |
3sai | 9DR | Dihydrofolate reductase | / | 0.447 | |
3zra | ORB | Progesterone receptor | / | 0.447 | |
4jtr | IBP | Aldo-keto reductase family 1 member C2 | / | 0.447 | |
4ysw | NAI | Xanthine dehydrogenase/oxidase | / | 0.447 | |
1odn | APV | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
1vzq | SHY | Prothrombin | 3.4.21.5 | 0.446 | |
2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.446 | |
3aos | JH2 | Hemolymph juvenile hormone binding protein | / | 0.446 | |
3fnu | 006 | HAP protein | / | 0.446 | |
3vv8 | B02 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
4at3 | LTI | BDNF/NT-3 growth factors receptor | 2.7.10.1 | 0.446 | |
4gts | 7TP | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.446 | |
4iyg | 1HU | Strictosidine synthase | 4.3.3.2 | 0.446 | |
4kbn | 25U | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
4li7 | 1XP | Tankyrase-1 | 2.4.2.30 | 0.446 | |
1jtu | LYB | Thymidylate synthase | / | 0.445 | |
1k27 | MTM | S-methyl-5'-thioadenosine phosphorylase | / | 0.445 | |
1rdt | L79 | Retinoic acid receptor RXR-alpha | / | 0.445 | |
1wdk | ACO | 3-ketoacyl-CoA thiolase | / | 0.445 | |
1yho | TRR | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
2bfa | CB3 | Pteridine reductase 1 | 1.5.1.33 | 0.445 | |
2gzl | 2AA | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | 4.6.1.12 | 0.445 | |
2w6z | L21 | Biotin carboxylase | 6.3.4.14 | 0.445 | |
3ans | S38 | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.445 | |
3b9l | AZZ | Serum albumin | / | 0.445 | |
3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
3gmd | 2M3 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.445 | |
3oap | REA | Retinoic acid receptor RXR-alpha | / | 0.445 | |
3v49 | PK0 | Androgen receptor | / | 0.445 | |
4gtt | 7TQ | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.445 | |
4lng | JAN | CaaX farnesyltransferase beta subunit Ram1 | / | 0.445 | |
4lsj | LSJ | Glucocorticoid receptor | / | 0.445 | |
1kce | CB3 | Thymidylate synthase | / | 0.444 | |
1kt5 | RTL | Retinol-binding protein 4 | / | 0.444 | |
1ohk | COP | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
1t47 | NTD | 4-hydroxyphenylpyruvate dioxygenase | 1.13.11.27 | 0.444 | |
1u0h | FOK | Adenylate cyclase type 2 | / | 0.444 | |
1u0h | FOK | Adenylate cyclase type 5 | / | 0.444 | |
1yqj | 6NP | Mitogen-activated protein kinase 14 | / | 0.444 | |
2aa2 | AS4 | Mineralocorticoid receptor | / | 0.444 | |
2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
3pgh | FLP | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.444 | |
4fcb | 0T7 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.444 | |
4k4f | K4F | Tankyrase-1 | 2.4.2.30 | 0.444 | |
4twn | B96 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.444 | |
1cju | FOK | Adenylate cyclase type 2 | / | 0.443 | |
1cju | FOK | Adenylate cyclase type 5 | / | 0.443 | |
1rx7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
1toi | HCI | Aspartate aminotransferase | 2.6.1.1 | 0.443 | |
2ouy | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.443 | |
3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.443 | |
3sig | AR6 | Uncharacterized protein | / | 0.443 | |
3wiz | LC6 | Bcl-2-like protein 1 | / | 0.443 | |
4ajd | F04 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.443 | |
4kd7 | 9DR | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
1fkx | PRH | Adenosine deaminase | 3.5.4.4 | 0.442 | |
1fw0 | KAI | Glutamate receptor 2 | / | 0.442 | |
2bf7 | HBI | Pteridine reductase 1 | 1.5.1.33 | 0.442 | |
2bp1 | NDP | Aflatoxin B1 aldehyde reductase member 2 | / | 0.442 | |
2fyu | FDN | Cytochrome b | / | 0.442 | |
2w3m | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
3rep | ATP | Integrin-linked protein kinase | 2.7.11.1 | 0.442 | |
4eil | FOL | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.442 | |
4wda | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.442 | |
1kqw | RTL | Cellular retinol-binding protein type II | / | 0.441 | |
1lke | DOG | Bilin-binding protein | / | 0.441 | |
1tox | NAD | Diphtheria toxin | / | 0.441 | |
1y2k | 7DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.441 | |
2fb8 | 215 | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.441 | |
2fm0 | M98 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.441 | |
2fpc | SCG | Strictosidine synthase | 4.3.3.2 | 0.441 | |
2hl2 | SSA | Threonine--tRNA ligase | 6.1.1.3 | 0.441 | |
3d80 | Q22 | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
3qn1 | A8S | Abscisic acid receptor PYR1 | / | 0.441 | |
4dsb | A8S | Abscisic acid receptor PYL3 | / | 0.441 | |
5cuq | NSC | Genome polyprotein | / | 0.441 | |
1cqp | 803 | Integrin alpha-L | / | 0.440 | |
1ldq | SHM | Avidin | / | 0.440 | |
1ori | SAH | Protein arginine N-methyltransferase 1 | / | 0.440 | |
1qnf | HDF | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.440 | |
1s9q | OHT | Estrogen-related receptor gamma | / | 0.440 | |
1std | BFS | Scytalone dehydratase | 4.2.1.94 | 0.440 | |
1uwh | BAX | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.440 | |
2aax | PDN | Mineralocorticoid receptor | / | 0.440 | |
2blc | CP7 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.440 | |
2f6r | ACO | Bifunctional coenzyme A synthase | / | 0.440 | |
2qhx | FE1 | Pteridine reductase 1 | 1.5.1.33 | 0.440 | |
2vqj | TFG | Histone deacetylase 4 | 3.5.1.98 | 0.440 | |
2zf4 | PPY | Uncharacterized protein | / | 0.440 | |
2zhw | 12U | Prothrombin | 3.4.21.5 | 0.440 | |
3itu | IBM | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.440 | |
3l3r | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
3zze | 6XP | Hepatocyte growth factor receptor | 2.7.10.1 | 0.440 | |
4g1n | NZT | Pyruvate kinase PKM | 2.7.1.40 | 0.440 | |
4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.440 | |
5dif | GNP | GTP-binding nuclear protein Ran | / | 0.440 |