sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
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 |
|---|---|---|---|
| 3utu | 1TS | Prothrombin | 3.4.21.5 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3utu | 1TS | Prothrombin | 3.4.21.5 | 1.000 | |
| 2zfr | 46U | Prothrombin | 3.4.21.5 | 0.735 | |
| 3p17 | 99P | Prothrombin | 3.4.21.5 | 0.702 | |
| 2zfq | 45U | Prothrombin | 3.4.21.5 | 0.687 | |
| 4ax9 | N5N | Prothrombin | 3.4.21.5 | 0.683 | |
| 3qto | 10P | Prothrombin | 3.4.21.5 | 0.669 | |
| 2zg0 | 50U | Prothrombin | 3.4.21.5 | 0.668 | |
| 3qwc | 98P | Prothrombin | 3.4.21.5 | 0.662 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.660 | |
| 4bao | MVF | Prothrombin | 3.4.21.5 | 0.660 | |
| 2bdy | UNB | Prothrombin | 3.4.21.5 | 0.654 | |
| 1gj5 | 130 | Prothrombin | 3.4.21.5 | 0.653 | |
| 1o2g | 696 | Prothrombin | 3.4.21.5 | 0.650 | |
| 2zhf | 49U | Prothrombin | 3.4.21.5 | 0.646 | |
| 2zhq | 27U | Prothrombin | 3.4.21.5 | 0.646 | |
| 2r2m | I50 | Prothrombin | 3.4.21.5 | 0.645 | |
| 1ype | UIP | Prothrombin | 3.4.21.5 | 0.641 | |
| 2anm | CDO | Prothrombin | 3.4.21.5 | 0.641 | |
| 3eq0 | 2TS | Prothrombin | 3.4.21.5 | 0.629 | |
| 1c4u | IH1 | Prothrombin | 3.4.21.5 | 0.626 | |
| 2zhw | 12U | Prothrombin | 3.4.21.5 | 0.626 | |
| 2zi2 | 24U | Prothrombin | 3.4.21.5 | 0.622 | |
| 3hat | GLY_VAL_ARG_RNG | Prothrombin | 3.4.21.5 | 0.622 | |
| 1ypm | RA4 | Prothrombin | 3.4.21.5 | 0.619 | |
| 1ghv | 120 | Prothrombin | 3.4.21.5 | 0.617 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.615 | |
| 2pks | G44 | Prothrombin | 3.4.21.5 | 0.615 | |
| 2zdv | 37U | Prothrombin | 3.4.21.5 | 0.615 | |
| 5cmx | 0G6 | Prothrombin | 3.4.21.5 | 0.614 | |
| 3biu | 10U | Prothrombin | 3.4.21.5 | 0.611 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.607 | |
| 1d4p | BPP | Prothrombin | 3.4.21.5 | 0.607 | |
| 2zff | 53U | Prothrombin | 3.4.21.5 | 0.605 | |
| 2zgx | 29U | Prothrombin | 3.4.21.5 | 0.605 | |
| 1ypj | UIB | Prothrombin | 3.4.21.5 | 0.602 | |
| 2znk | 31U | Prothrombin | 3.4.21.5 | 0.599 | |
| 3qtv | 06P | Prothrombin | 3.4.21.5 | 0.599 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.597 | |
| 2v3h | I25 | Prothrombin | 3.4.21.5 | 0.595 | |
| 1oyt | FSN | Prothrombin | 3.4.21.5 | 0.590 | |
| 1c4y | IH3 | Prothrombin | 3.4.21.5 | 0.589 | |
| 3dux | 64U | Prothrombin | 3.4.21.5 | 0.589 | |
| 4ayy | 9MX | Prothrombin | 3.4.21.5 | 0.589 | |
| 4az2 | 9MU | Prothrombin | 3.4.21.5 | 0.588 | |
| 1mue | CDD | Prothrombin | 3.4.21.5 | 0.586 | |
| 1vzq | SHY | Prothrombin | 3.4.21.5 | 0.585 | |
| 2zfp | 19U | Prothrombin | 3.4.21.5 | 0.585 | |
| 1afe | ALZ | Prothrombin | 3.4.21.5 | 0.584 | |
| 1o5g | CR9 | Prothrombin | 3.4.21.5 | 0.584 | |
| 3c27 | DKK | Prothrombin | 3.4.21.5 | 0.584 | |
| 4bak | M67 | Prothrombin | 3.4.21.5 | 0.583 | |
| 7kme | ACE_0BN_CHG_PRR | Prothrombin | 3.4.21.5 | 0.583 | |
| 1bcu | PRL | Prothrombin | 3.4.21.5 | 0.580 | |
| 1k21 | IGN | Prothrombin | 3.4.21.5 | 0.580 | |
| 2cf8 | ESH | Prothrombin | 3.4.21.5 | 0.580 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.579 | |
| 4baq | M4Z | Prothrombin | 3.4.21.5 | 0.579 | |
| 1d9i | 00P | Prothrombin | 3.4.21.5 | 0.577 | |
| 2v3o | I26 | Prothrombin | 3.4.21.5 | 0.577 | |
| 1a4w | QWE | Prothrombin | 3.4.21.5 | 0.576 | |
| 2jh6 | 894 | Prothrombin | 3.4.21.5 | 0.575 | |
| 2uuk | 897 | Prothrombin | 3.4.21.5 | 0.575 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.575 | |
| 2bxt | C2D | Prothrombin | 3.4.21.5 | 0.574 | |
| 2zgb | 21U | Prothrombin | 3.4.21.5 | 0.574 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.573 | |
| 1t4v | 14A | Prothrombin | 3.4.21.5 | 0.572 | |
| 1zrb | 062 | Prothrombin | 3.4.21.5 | 0.572 | |
| 1nzq | 162 | Prothrombin | 3.4.21.5 | 0.571 | |
| 2zhe | 13U | Prothrombin | 3.4.21.5 | 0.570 | |
| 1ypl | RA8 | Prothrombin | 3.4.21.5 | 0.569 | |
| 4ban | M6S | Prothrombin | 3.4.21.5 | 0.567 | |
| 4bah | MEL | Prothrombin | 3.4.21.5 | 0.566 | |
| 1uma | IN2 | Prothrombin | 3.4.21.5 | 0.564 | |
| 1zgv | 501 | Prothrombin | 3.4.21.5 | 0.564 | |
| 1mu6 | CDA | Prothrombin | 3.4.21.5 | 0.562 | |
| 1t4u | 81A | Prothrombin | 3.4.21.5 | 0.561 | |
| 2uuj | 896 | Prothrombin | 3.4.21.5 | 0.554 | |
| 1ae8 | AZL | Prothrombin | 3.4.21.5 | 0.552 | |
| 1xm1 | GAH | Prothrombin | 3.4.21.5 | 0.552 | |
| 4bam | MM9 | Prothrombin | 3.4.21.5 | 0.550 | |
| 4e7r | 0NW | Prothrombin | 3.4.21.5 | 0.548 | |
| 1sb1 | 165 | Prothrombin | 3.4.21.5 | 0.546 | |
| 1ypk | CCR | Prothrombin | 3.4.21.5 | 0.545 | |
| 2zda | 32U | Prothrombin | 3.4.21.5 | 0.542 | |
| 1c1u | BAI | Prothrombin | 3.4.21.5 | 0.539 | |
| 4lxb | 7R9 | Prothrombin | 3.4.21.5 | 0.536 | |
| 1riw | OSC | Prothrombin | 3.4.21.5 | 0.535 | |
| 1zgi | 382 | Prothrombin | 3.4.21.5 | 0.534 | |
| 2cf9 | 348 | Prothrombin | 3.4.21.5 | 0.533 | |
| 2zf0 | 51U | Prothrombin | 3.4.21.5 | 0.519 | |
| 3biv | 11U | Prothrombin | 3.4.21.5 | 0.508 | |
| 1d6w | 00R | Prothrombin | 3.4.21.5 | 0.505 | |
| 2pvj | P44 | Casein kinase II subunit alpha | 2.7.11.1 | 0.485 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.476 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.476 | |
| 1c3x | 8IG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.475 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.474 | |
| 1c1w | BAH | Prothrombin | 3.4.21.5 | 0.472 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.472 | |
| 3mau | PLR | Putative sphingosine-1-phosphate lyase | / | 0.471 | |
| 1lf2 | R37 | Plasmepsin-2 | 3.4.23.39 | 0.466 | |
| 3k5g | BJC | Beta-secretase 1 | 3.4.23.46 | 0.465 | |
| 1n95 | HFP | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.464 | |
| 1n95 | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.464 | |
| 1qo8 | FAD | Fumarate reductase flavoprotein subunit | / | 0.464 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.464 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.464 | |
| 2fhl | BNI | Avidin-related protein 4/5 | / | 0.463 | |
| 3dop | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.462 | |
| 3mb7 | 14I | Casein kinase II subunit alpha | 2.7.11.1 | 0.462 | |
| 3exf | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.459 | |
| 3exf | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.459 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.459 | |
| 2wf1 | ZY1 | Beta-secretase 1 | 3.4.23.46 | 0.458 | |
| 2wf3 | ZY3 | Beta-secretase 1 | 3.4.23.46 | 0.458 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.458 | |
| 2ziq | 26U | Prothrombin | 3.4.21.5 | 0.457 | |
| 1eji | THF | Serine hydroxymethyltransferase, cytosolic | / | 0.456 | |
| 1ju2 | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.455 | |
| 2b8l | 5HA | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 2iya | ZIO | Oleandomycin glycosyltransferase | / | 0.455 | |
| 2vjm | COA | Formyl-CoA:oxalate CoA-transferase | / | 0.454 | |
| 3uxv | GUN | NADPH-dependent 7-cyano-7-deazaguanine reductase | / | 0.454 | |
| 4r1l | ADP | Phenylacetate-coenzyme A ligase | / | 0.453 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 4l33 | F70 | Tankyrase-2 | 2.4.2.30 | 0.452 | |
| 1xs7 | MMI | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 2pk3 | A2R | GDP-6-deoxy-D-mannose reductase | / | 0.451 | |
| 3v0p | 4GW | Histo-blood group ABO system transferase | / | 0.451 | |
| 4dh6 | 0KN | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 4jtq | NAP | Aldo-keto reductase family 1 member C2 | / | 0.451 | |
| 4kwc | SAH | Methyltransferase domain family | / | 0.451 | |
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.450 | |
| 2iqg | F2I | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 4gtv | 7TR | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.450 | |
| 1y7l | ASN_LEU_ASN_ILE | Cysteine synthase | 2.5.1.47 | 0.449 | |
| 4z28 | BTN | Hoefavidin | / | 0.449 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.448 | |
| 3vy2 | FMN | FMN-binding protein | / | 0.448 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.447 | |
| 4d03 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.447 | |
| 4eua | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.447 | |
| 5c3a | URM | Histo-blood group ABO system transferase | / | 0.447 | |
| 2vnn | CM7 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 3bv7 | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.446 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 3lq4 | TDP | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.446 | |
| 3qgf | 46F | Genome polyprotein | 2.7.7.48 | 0.446 | |
| 4bux | F35 | Tankyrase-2 | 2.4.2.30 | 0.446 | |
| 5ig2 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.446 | |
| 1c7o | PPG | Hemolysin | / | 0.445 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.445 | |
| 4emd | C5P | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.445 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.445 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 3pe2 | E1B | Casein kinase II subunit alpha | 2.7.11.1 | 0.444 | |
| 2ejz | SAH | Diphthine synthase | / | 0.443 | |
| 2ign | FAD | Pyranose 2-oxidase | / | 0.443 | |
| 2ntr | L00 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3duy | AFJ | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3g4g | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.443 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.442 | |
| 2r5n | TPP | Transketolase 1 | / | 0.442 | |
| 2vmy | FFO | Serine hydroxymethyltransferase | / | 0.442 | |
| 3gl2 | D3M | DdmC | / | 0.442 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3nu0 | 3TU | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 4yry | FAD | Glutamate synthase, beta subunit | / | 0.442 | |
| 4ytn | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.442 | |
| 1fw0 | KAI | Glutamate receptor 2 | / | 0.441 | |
| 1mjb | ACO | Histone acetyltransferase ESA1 | / | 0.441 | |
| 1tkc | M6T | Transketolase 1 | 2.2.1.1 | 0.441 | |
| 2hiz | LIJ | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.441 | |
| 1c4v | IH2 | Prothrombin | 3.4.21.5 | 0.440 | |
| 1flm | FMN | FMN-binding protein | / | 0.440 | |
| 1so2 | 666 | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.440 | |
| 2hdj | NDP | Aldo-keto reductase family 1 member C2 | / | 0.440 | |
| 2wf2 | ZY2 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3g1r | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.440 | |
| 3wzn | BTN | Streptavidin | / | 0.440 | |
| 4eph | 0RK | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.440 | |
| 4k8s | 1QT | Beta-secretase 1 | 3.4.23.46 | 0.440 |