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 |
|---|---|---|---|
| 2zhw | 12U | Prothrombin | 3.4.21.5 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2zhw | 12U | Prothrombin | 3.4.21.5 | 1.000 | |
| 3qwc | 98P | Prothrombin | 3.4.21.5 | 0.735 | |
| 2zfr | 46U | Prothrombin | 3.4.21.5 | 0.719 | |
| 2zhf | 49U | Prothrombin | 3.4.21.5 | 0.710 | |
| 2zgx | 29U | Prothrombin | 3.4.21.5 | 0.694 | |
| 1ypm | RA4 | Prothrombin | 3.4.21.5 | 0.689 | |
| 1ypj | UIB | Prothrombin | 3.4.21.5 | 0.688 | |
| 4bah | MEL | Prothrombin | 3.4.21.5 | 0.687 | |
| 2r2m | I50 | Prothrombin | 3.4.21.5 | 0.685 | |
| 1gj5 | 130 | Prothrombin | 3.4.21.5 | 0.684 | |
| 2zfp | 19U | Prothrombin | 3.4.21.5 | 0.684 | |
| 3hat | GLY_VAL_ARG_RNG | Prothrombin | 3.4.21.5 | 0.682 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.677 | |
| 1ghv | 120 | Prothrombin | 3.4.21.5 | 0.677 | |
| 1o2g | 696 | Prothrombin | 3.4.21.5 | 0.673 | |
| 4bao | MVF | Prothrombin | 3.4.21.5 | 0.673 | |
| 3p17 | 99P | Prothrombin | 3.4.21.5 | 0.669 | |
| 2anm | CDO | Prothrombin | 3.4.21.5 | 0.668 | |
| 2v3h | I25 | Prothrombin | 3.4.21.5 | 0.667 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.666 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.664 | |
| 2pks | G44 | Prothrombin | 3.4.21.5 | 0.664 | |
| 1ypl | RA8 | Prothrombin | 3.4.21.5 | 0.657 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.654 | |
| 3biu | 10U | Prothrombin | 3.4.21.5 | 0.654 | |
| 4ayy | 9MX | Prothrombin | 3.4.21.5 | 0.653 | |
| 2zdv | 37U | Prothrombin | 3.4.21.5 | 0.652 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.652 | |
| 2zhq | 27U | Prothrombin | 3.4.21.5 | 0.651 | |
| 2bdy | UNB | Prothrombin | 3.4.21.5 | 0.648 | |
| 2zff | 53U | Prothrombin | 3.4.21.5 | 0.645 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.641 | |
| 1zgi | 382 | Prothrombin | 3.4.21.5 | 0.639 | |
| 1bcu | PRL | Prothrombin | 3.4.21.5 | 0.638 | |
| 2zhe | 13U | Prothrombin | 3.4.21.5 | 0.638 | |
| 1k22 | MEL | Prothrombin | 3.4.21.5 | 0.637 | |
| 3eq0 | 2TS | Prothrombin | 3.4.21.5 | 0.637 | |
| 2zg0 | 50U | Prothrombin | 3.4.21.5 | 0.636 | |
| 2jh5 | 895 | Prothrombin | 3.4.21.5 | 0.633 | |
| 1d9i | 00P | Prothrombin | 3.4.21.5 | 0.631 | |
| 2zgb | 21U | Prothrombin | 3.4.21.5 | 0.631 | |
| 3qto | 10P | Prothrombin | 3.4.21.5 | 0.631 | |
| 1xm1 | GAH | Prothrombin | 3.4.21.5 | 0.626 | |
| 3dux | 64U | Prothrombin | 3.4.21.5 | 0.626 | |
| 2uuk | 897 | Prothrombin | 3.4.21.5 | 0.624 | |
| 1t4v | 14A | Prothrombin | 3.4.21.5 | 0.621 | |
| 1o5g | CR9 | Prothrombin | 3.4.21.5 | 0.620 | |
| 4ax9 | N5N | Prothrombin | 3.4.21.5 | 0.620 | |
| 4lxb | 7R9 | Prothrombin | 3.4.21.5 | 0.619 | |
| 1sb1 | 165 | Prothrombin | 3.4.21.5 | 0.618 | |
| 2zf0 | 51U | Prothrombin | 3.4.21.5 | 0.616 | |
| 1vzq | SHY | Prothrombin | 3.4.21.5 | 0.615 | |
| 1c1u | BAI | Prothrombin | 3.4.21.5 | 0.614 | |
| 1t4u | 81A | Prothrombin | 3.4.21.5 | 0.613 | |
| 2v3o | I26 | Prothrombin | 3.4.21.5 | 0.613 | |
| 1d6w | 00R | Prothrombin | 3.4.21.5 | 0.612 | |
| 2jh6 | 894 | Prothrombin | 3.4.21.5 | 0.612 | |
| 1mue | CDD | Prothrombin | 3.4.21.5 | 0.611 | |
| 3qtv | 06P | Prothrombin | 3.4.21.5 | 0.611 | |
| 1ype | UIP | Prothrombin | 3.4.21.5 | 0.609 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.608 | |
| 1d4p | BPP | Prothrombin | 3.4.21.5 | 0.605 | |
| 2cf8 | ESH | Prothrombin | 3.4.21.5 | 0.603 | |
| 1c4y | IH3 | Prothrombin | 3.4.21.5 | 0.601 | |
| 1nzq | 162 | Prothrombin | 3.4.21.5 | 0.600 | |
| 2znk | 31U | Prothrombin | 3.4.21.5 | 0.599 | |
| 1afe | ALZ | Prothrombin | 3.4.21.5 | 0.598 | |
| 1zrb | 062 | Prothrombin | 3.4.21.5 | 0.595 | |
| 2uuj | 896 | Prothrombin | 3.4.21.5 | 0.594 | |
| 1uma | IN2 | Prothrombin | 3.4.21.5 | 0.592 | |
| 4e7r | 0NW | Prothrombin | 3.4.21.5 | 0.591 | |
| 4bak | M67 | Prothrombin | 3.4.21.5 | 0.590 | |
| 2cf9 | 348 | Prothrombin | 3.4.21.5 | 0.589 | |
| 1ypk | CCR | Prothrombin | 3.4.21.5 | 0.587 | |
| 1ae8 | AZL | Prothrombin | 3.4.21.5 | 0.585 | |
| 4bam | MM9 | Prothrombin | 3.4.21.5 | 0.584 | |
| 1mu6 | CDA | Prothrombin | 3.4.21.5 | 0.583 | |
| 2zfq | 45U | Prothrombin | 3.4.21.5 | 0.578 | |
| 3utu | 1TS | Prothrombin | 3.4.21.5 | 0.578 | |
| 5cmx | 0G6 | Prothrombin | 3.4.21.5 | 0.578 | |
| 1k21 | IGN | Prothrombin | 3.4.21.5 | 0.577 | |
| 4az2 | 9MU | Prothrombin | 3.4.21.5 | 0.575 | |
| 1zgv | 501 | Prothrombin | 3.4.21.5 | 0.573 | |
| 1a4w | QWE | Prothrombin | 3.4.21.5 | 0.571 | |
| 4ban | M6S | Prothrombin | 3.4.21.5 | 0.563 | |
| 4baq | M4Z | Prothrombin | 3.4.21.5 | 0.558 | |
| 1w7g | MIU | Prothrombin | 3.4.21.5 | 0.554 | |
| 3c27 | DKK | Prothrombin | 3.4.21.5 | 0.551 | |
| 1riw | OSC | Prothrombin | 3.4.21.5 | 0.550 | |
| 2bxt | C2D | Prothrombin | 3.4.21.5 | 0.548 | |
| 7kme | ACE_0BN_CHG_PRR | Prothrombin | 3.4.21.5 | 0.548 | |
| 1c4v | IH2 | Prothrombin | 3.4.21.5 | 0.543 | |
| 2bvs | 2CE | Prothrombin | 3.4.21.5 | 0.540 | |
| 4ayv | 9MQ | Prothrombin | 3.4.21.5 | 0.532 | |
| 1ny2 | ARG_PRO_PRO_GLY | Prothrombin | 3.4.21.5 | 0.500 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.496 | |
| 3qdz | PRO_ALA_PRO_ARG | Prothrombin | 3.4.21.5 | 0.491 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.490 | |
| 1gj4 | 132 | Prothrombin | 3.4.21.5 | 0.488 | |
| 4loy | 6XS | Prothrombin | 3.4.21.5 | 0.486 | |
| 1o0d | 163 | Prothrombin | 3.4.21.5 | 0.484 | |
| 1oyt | FSN | Prothrombin | 3.4.21.5 | 0.479 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.479 | |
| 1mu8 | CDB | Prothrombin | 3.4.21.5 | 0.474 | |
| 1c5n | ESI | Prothrombin | 3.4.21.5 | 0.469 | |
| 3eks | CY9 | Actin-5C | / | 0.468 | |
| 3own | 3OW | Renin | 3.4.23.15 | 0.467 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.466 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.464 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.463 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.462 | |
| 1c4u | IH1 | Prothrombin | 3.4.21.5 | 0.459 | |
| 3eku | CY9 | Actin-5C | / | 0.459 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.459 | |
| 5c6c | CMP | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.459 | |
| 3mau | PLR | Putative sphingosine-1-phosphate lyase | / | 0.458 | |
| 3zw9 | NAD | Peroxisomal bifunctional enzyme | 1.1.1.35 | 0.458 | |
| 3e34 | ED1 | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.457 | |
| 3e34 | ED1 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.457 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.457 | |
| 4h6p | FMN | Chromate reductase | / | 0.457 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.456 | |
| 2gyw | OBI | Acetylcholinesterase | 3.1.1.7 | 0.456 | |
| 2iqg | F2I | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.456 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.455 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.455 | |
| 1qoq | IGP | Tryptophan synthase alpha chain | / | 0.455 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.455 | |
| 4jtq | NAP | Aldo-keto reductase family 1 member C2 | / | 0.455 | |
| 2xlt | NA0 | Putative flavin-containing monooxygenase | / | 0.454 | |
| 1jtv | TES | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.453 | |
| 1ndi | COA | Carnitine O-acetyltransferase | 2.3.1.7 | 0.453 | |
| 2ziq | 26U | Prothrombin | 3.4.21.5 | 0.453 | |
| 2vat | COA | Acetyl-CoA--deacetylcephalosporin C acetyltransferase | 2.3.1.175 | 0.452 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.452 | |
| 2wf3 | ZY3 | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.451 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.450 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.448 | |
| 3biv | 11U | Prothrombin | 3.4.21.5 | 0.448 | |
| 1ta2 | 176 | Prothrombin | 3.4.21.5 | 0.447 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.447 | |
| 3ihz | FK5 | Peptidylprolyl isomerase | / | 0.447 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.447 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.447 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.446 | |
| 2xlp | NAP | Putative flavin-containing monooxygenase | / | 0.446 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.444 | |
| 2aq7 | TL5 | 3-oxoacyl-[acyl-carrier-protein] synthase 1 | 2.3.1.41 | 0.444 | |
| 4zu4 | 4TG | WxcM-like protein | / | 0.444 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3zht | TD9 | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.443 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.442 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.442 | |
| 3g4g | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.442 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.442 | |
| 2op1 | 8PC | Enoyl-ACP reductase | / | 0.441 | |
| 2uyw | BTN | Avd protein | / | 0.441 | |
| 2z3n | PHE_ARG_TYR_LEU_GLY | Leucyl/phenylalanyl-tRNA--protein transferase | 2.3.2.6 | 0.441 | |
| 3fhx | PXL | Pyridoxal kinase | 2.7.1.35 | 0.441 | |
| 1h69 | ARH | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.440 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.440 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 5fd8 | A5A | Putative carboxypeptidase yocD | / | 0.440 |