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 |
|---|---|---|---|
| 2bdy | UNB | Prothrombin | 3.4.21.5 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2bdy | UNB | Prothrombin | 3.4.21.5 | 1.000 | |
| 1d4p | BPP | Prothrombin | 3.4.21.5 | 0.696 | |
| 4ax9 | N5N | Prothrombin | 3.4.21.5 | 0.665 | |
| 2pks | G44 | Prothrombin | 3.4.21.5 | 0.662 | |
| 2r2m | I50 | Prothrombin | 3.4.21.5 | 0.657 | |
| 2uuk | 897 | Prothrombin | 3.4.21.5 | 0.649 | |
| 2zfr | 46U | Prothrombin | 3.4.21.5 | 0.643 | |
| 1ypm | RA4 | Prothrombin | 3.4.21.5 | 0.642 | |
| 2jh5 | 895 | Prothrombin | 3.4.21.5 | 0.642 | |
| 1ypj | UIB | Prothrombin | 3.4.21.5 | 0.641 | |
| 1xm1 | GAH | Prothrombin | 3.4.21.5 | 0.640 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.639 | |
| 2zhq | 27U | Prothrombin | 3.4.21.5 | 0.639 | |
| 1ype | UIP | Prothrombin | 3.4.21.5 | 0.637 | |
| 3hat | GLY_VAL_ARG_RNG | Prothrombin | 3.4.21.5 | 0.637 | |
| 1d9i | 00P | Prothrombin | 3.4.21.5 | 0.635 | |
| 2cf8 | ESH | Prothrombin | 3.4.21.5 | 0.635 | |
| 2anm | CDO | Prothrombin | 3.4.21.5 | 0.634 | |
| 3qwc | 98P | Prothrombin | 3.4.21.5 | 0.634 | |
| 1t4u | 81A | Prothrombin | 3.4.21.5 | 0.629 | |
| 2zhf | 49U | Prothrombin | 3.4.21.5 | 0.629 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.628 | |
| 1gj5 | 130 | Prothrombin | 3.4.21.5 | 0.628 | |
| 1t4v | 14A | Prothrombin | 3.4.21.5 | 0.628 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.622 | |
| 2v3o | I26 | Prothrombin | 3.4.21.5 | 0.622 | |
| 1ta6 | 177 | Prothrombin | 3.4.21.5 | 0.620 | |
| 2v3h | I25 | Prothrombin | 3.4.21.5 | 0.620 | |
| 1bcu | PRL | Prothrombin | 3.4.21.5 | 0.619 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.617 | |
| 1o2g | 696 | Prothrombin | 3.4.21.5 | 0.615 | |
| 2zfp | 19U | Prothrombin | 3.4.21.5 | 0.612 | |
| 2zhw | 12U | Prothrombin | 3.4.21.5 | 0.612 | |
| 1ghv | 120 | Prothrombin | 3.4.21.5 | 0.609 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.609 | |
| 2zda | 32U | Prothrombin | 3.4.21.5 | 0.605 | |
| 1c4y | IH3 | Prothrombin | 3.4.21.5 | 0.603 | |
| 1sb1 | 165 | Prothrombin | 3.4.21.5 | 0.602 | |
| 4ayy | 9MX | Prothrombin | 3.4.21.5 | 0.602 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.599 | |
| 2zfq | 45U | Prothrombin | 3.4.21.5 | 0.595 | |
| 4bah | MEL | Prothrombin | 3.4.21.5 | 0.594 | |
| 1ypl | RA8 | Prothrombin | 3.4.21.5 | 0.593 | |
| 2jh6 | 894 | Prothrombin | 3.4.21.5 | 0.593 | |
| 2zgx | 29U | Prothrombin | 3.4.21.5 | 0.593 | |
| 3p17 | 99P | Prothrombin | 3.4.21.5 | 0.593 | |
| 3eq0 | 2TS | Prothrombin | 3.4.21.5 | 0.590 | |
| 1c4u | IH1 | Prothrombin | 3.4.21.5 | 0.586 | |
| 1zgv | 501 | Prothrombin | 3.4.21.5 | 0.586 | |
| 3utu | 1TS | Prothrombin | 3.4.21.5 | 0.586 | |
| 1mu6 | CDA | Prothrombin | 3.4.21.5 | 0.585 | |
| 3biu | 10U | Prothrombin | 3.4.21.5 | 0.584 | |
| 1o5g | CR9 | Prothrombin | 3.4.21.5 | 0.583 | |
| 2zgb | 21U | Prothrombin | 3.4.21.5 | 0.582 | |
| 1vzq | SHY | Prothrombin | 3.4.21.5 | 0.579 | |
| 4lxb | 7R9 | Prothrombin | 3.4.21.5 | 0.574 | |
| 2zc9 | 22U | Prothrombin | 3.4.21.5 | 0.572 | |
| 2znk | 31U | Prothrombin | 3.4.21.5 | 0.572 | |
| 2zdv | 37U | Prothrombin | 3.4.21.5 | 0.571 | |
| 2zg0 | 50U | Prothrombin | 3.4.21.5 | 0.571 | |
| 1oyt | FSN | Prothrombin | 3.4.21.5 | 0.569 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.569 | |
| 4bao | MVF | Prothrombin | 3.4.21.5 | 0.568 | |
| 4e7r | 0NW | Prothrombin | 3.4.21.5 | 0.568 | |
| 1ae8 | AZL | Prothrombin | 3.4.21.5 | 0.567 | |
| 1mue | CDD | Prothrombin | 3.4.21.5 | 0.567 | |
| 5cmx | 0G6 | Prothrombin | 3.4.21.5 | 0.567 | |
| 1zgi | 382 | Prothrombin | 3.4.21.5 | 0.566 | |
| 3qto | 10P | Prothrombin | 3.4.21.5 | 0.563 | |
| 2cf9 | 348 | Prothrombin | 3.4.21.5 | 0.562 | |
| 2zhe | 13U | Prothrombin | 3.4.21.5 | 0.560 | |
| 2zf0 | 51U | Prothrombin | 3.4.21.5 | 0.558 | |
| 1d6w | 00R | Prothrombin | 3.4.21.5 | 0.557 | |
| 2zff | 53U | Prothrombin | 3.4.21.5 | 0.557 | |
| 1ypk | CCR | Prothrombin | 3.4.21.5 | 0.554 | |
| 2uuj | 896 | Prothrombin | 3.4.21.5 | 0.551 | |
| 3c27 | DKK | Prothrombin | 3.4.21.5 | 0.551 | |
| 3qtv | 06P | Prothrombin | 3.4.21.5 | 0.550 | |
| 7kme | ACE_0BN_CHG_PRR | Prothrombin | 3.4.21.5 | 0.549 | |
| 2jh0 | 701 | Prothrombin | 3.4.21.5 | 0.542 | |
| 1uma | IN2 | Prothrombin | 3.4.21.5 | 0.541 | |
| 1k22 | MEL | Prothrombin | 3.4.21.5 | 0.538 | |
| 1zrb | 062 | Prothrombin | 3.4.21.5 | 0.538 | |
| 1c4v | IH2 | Prothrombin | 3.4.21.5 | 0.536 | |
| 1afe | ALZ | Prothrombin | 3.4.21.5 | 0.534 | |
| 3dux | 64U | Prothrombin | 3.4.21.5 | 0.534 | |
| 4az2 | 9MU | Prothrombin | 3.4.21.5 | 0.533 | |
| 1k21 | IGN | Prothrombin | 3.4.21.5 | 0.532 | |
| 4bam | MM9 | Prothrombin | 3.4.21.5 | 0.530 | |
| 4bak | M67 | Prothrombin | 3.4.21.5 | 0.529 | |
| 1a4w | QWE | Prothrombin | 3.4.21.5 | 0.527 | |
| 1nzq | 162 | Prothrombin | 3.4.21.5 | 0.527 | |
| 1riw | OSC | Prothrombin | 3.4.21.5 | 0.526 | |
| 2zi2 | 24U | Prothrombin | 3.4.21.5 | 0.519 | |
| 2bxt | C2D | Prothrombin | 3.4.21.5 | 0.518 | |
| 4ayv | 9MQ | Prothrombin | 3.4.21.5 | 0.514 | |
| 1c1u | BAI | Prothrombin | 3.4.21.5 | 0.510 | |
| 1w7g | MIU | Prothrombin | 3.4.21.5 | 0.510 | |
| 4rn6 | 15U | Prothrombin | 3.4.21.5 | 0.510 | |
| 3qdz | PRO_ALA_PRO_ARG | Prothrombin | 3.4.21.5 | 0.495 | |
| 4ban | M6S | Prothrombin | 3.4.21.5 | 0.492 | |
| 4baq | M4Z | Prothrombin | 3.4.21.5 | 0.489 | |
| 1kts | C24 | Prothrombin | 3.4.21.5 | 0.474 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.473 | |
| 1c5n | ESI | Prothrombin | 3.4.21.5 | 0.467 | |
| 1ny2 | ARG_PRO_PRO_GLY | Prothrombin | 3.4.21.5 | 0.467 | |
| 1ju2 | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.463 | |
| 3exf | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.462 | |
| 3exf | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.462 | |
| 1o0d | 163 | Prothrombin | 3.4.21.5 | 0.459 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.458 | |
| 4jtq | NAP | Aldo-keto reductase family 1 member C2 | / | 0.458 | |
| 1qoq | IGP | Tryptophan synthase alpha chain | / | 0.457 | |
| 2ziq | 26U | Prothrombin | 3.4.21.5 | 0.456 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.455 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.454 | |
| 4b11 | 7I1 | Glycylpeptide N-tetradecanoyltransferase | / | 0.452 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.452 | |
| 1mu8 | CDB | Prothrombin | 3.4.21.5 | 0.450 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.450 | |
| 1c1w | BAH | Prothrombin | 3.4.21.5 | 0.448 | |
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.448 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.447 | |
| 4btt | VYR | Coagulation factor X | 3.4.21.6 | 0.444 | |
| 2i65 | NAD | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.443 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.442 | |
| 4kbz | 1QA | Egl nine homolog 1 | / | 0.441 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 4h6p | FMN | Chromate reductase | / | 0.440 |