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 |
|---|---|---|---|
| 3eq0 | 2TS | Prothrombin | 3.4.21.5 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3eq0 | 2TS | Prothrombin | 3.4.21.5 | 1.000 | |
| 2zgb | 21U | Prothrombin | 3.4.21.5 | 0.836 | |
| 3dux | 64U | Prothrombin | 3.4.21.5 | 0.826 | |
| 4bam | MM9 | Prothrombin | 3.4.21.5 | 0.792 | |
| 2zgx | 29U | Prothrombin | 3.4.21.5 | 0.773 | |
| 2zc9 | 22U | Prothrombin | 3.4.21.5 | 0.768 | |
| 2zf0 | 51U | Prothrombin | 3.4.21.5 | 0.761 | |
| 2znk | 31U | Prothrombin | 3.4.21.5 | 0.752 | |
| 2zdv | 37U | Prothrombin | 3.4.21.5 | 0.748 | |
| 4bak | M67 | Prothrombin | 3.4.21.5 | 0.743 | |
| 2zhq | 27U | Prothrombin | 3.4.21.5 | 0.739 | |
| 7kme | ACE_0BN_CHG_PRR | Prothrombin | 3.4.21.5 | 0.734 | |
| 2zhe | 13U | Prothrombin | 3.4.21.5 | 0.732 | |
| 2zhf | 49U | Prothrombin | 3.4.21.5 | 0.731 | |
| 3biu | 10U | Prothrombin | 3.4.21.5 | 0.730 | |
| 2zff | 53U | Prothrombin | 3.4.21.5 | 0.725 | |
| 4baq | M4Z | Prothrombin | 3.4.21.5 | 0.723 | |
| 3hat | GLY_VAL_ARG_RNG | Prothrombin | 3.4.21.5 | 0.720 | |
| 1zrb | 062 | Prothrombin | 3.4.21.5 | 0.719 | |
| 4ban | M6S | Prothrombin | 3.4.21.5 | 0.711 | |
| 1t4v | 14A | Prothrombin | 3.4.21.5 | 0.710 | |
| 4bah | MEL | Prothrombin | 3.4.21.5 | 0.696 | |
| 2zg0 | 50U | Prothrombin | 3.4.21.5 | 0.692 | |
| 1d4p | BPP | Prothrombin | 3.4.21.5 | 0.690 | |
| 2zfq | 45U | Prothrombin | 3.4.21.5 | 0.689 | |
| 2zfr | 46U | Prothrombin | 3.4.21.5 | 0.688 | |
| 2r2m | I50 | Prothrombin | 3.4.21.5 | 0.685 | |
| 4bao | MVF | Prothrombin | 3.4.21.5 | 0.684 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.680 | |
| 1t4u | 81A | Prothrombin | 3.4.21.5 | 0.673 | |
| 1ae8 | AZL | Prothrombin | 3.4.21.5 | 0.672 | |
| 2zfp | 19U | Prothrombin | 3.4.21.5 | 0.670 | |
| 1mue | CDD | Prothrombin | 3.4.21.5 | 0.669 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.668 | |
| 1afe | ALZ | Prothrombin | 3.4.21.5 | 0.667 | |
| 1d6w | 00R | Prothrombin | 3.4.21.5 | 0.667 | |
| 1vzq | SHY | Prothrombin | 3.4.21.5 | 0.663 | |
| 3c27 | DKK | Prothrombin | 3.4.21.5 | 0.662 | |
| 1k21 | IGN | Prothrombin | 3.4.21.5 | 0.661 | |
| 1c4u | IH1 | Prothrombin | 3.4.21.5 | 0.658 | |
| 2anm | CDO | Prothrombin | 3.4.21.5 | 0.651 | |
| 2pks | G44 | Prothrombin | 3.4.21.5 | 0.650 | |
| 1mu6 | CDA | Prothrombin | 3.4.21.5 | 0.641 | |
| 2zhw | 12U | Prothrombin | 3.4.21.5 | 0.641 | |
| 1sb1 | 165 | Prothrombin | 3.4.21.5 | 0.639 | |
| 1ta6 | 177 | Prothrombin | 3.4.21.5 | 0.639 | |
| 2bdy | UNB | Prothrombin | 3.4.21.5 | 0.639 | |
| 1ypl | RA8 | Prothrombin | 3.4.21.5 | 0.637 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.636 | |
| 1bcu | PRL | Prothrombin | 3.4.21.5 | 0.635 | |
| 2uuk | 897 | Prothrombin | 3.4.21.5 | 0.633 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.630 | |
| 1nzq | 162 | Prothrombin | 3.4.21.5 | 0.629 | |
| 1ypj | UIB | Prothrombin | 3.4.21.5 | 0.628 | |
| 3p17 | 99P | Prothrombin | 3.4.21.5 | 0.627 | |
| 1zgv | 501 | Prothrombin | 3.4.21.5 | 0.622 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.619 | |
| 3qto | 10P | Prothrombin | 3.4.21.5 | 0.616 | |
| 1ypm | RA4 | Prothrombin | 3.4.21.5 | 0.612 | |
| 2cf9 | 348 | Prothrombin | 3.4.21.5 | 0.611 | |
| 2jh5 | 895 | Prothrombin | 3.4.21.5 | 0.610 | |
| 4ayy | 9MX | Prothrombin | 3.4.21.5 | 0.609 | |
| 1a4w | QWE | Prothrombin | 3.4.21.5 | 0.608 | |
| 1ypk | CCR | Prothrombin | 3.4.21.5 | 0.607 | |
| 2uuj | 896 | Prothrombin | 3.4.21.5 | 0.607 | |
| 1c4y | IH3 | Prothrombin | 3.4.21.5 | 0.604 | |
| 1d9i | 00P | Prothrombin | 3.4.21.5 | 0.602 | |
| 2jh6 | 894 | Prothrombin | 3.4.21.5 | 0.600 | |
| 3biv | 11U | Prothrombin | 3.4.21.5 | 0.597 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.596 | |
| 3qwc | 98P | Prothrombin | 3.4.21.5 | 0.596 | |
| 1ghv | 120 | Prothrombin | 3.4.21.5 | 0.593 | |
| 1xm1 | GAH | Prothrombin | 3.4.21.5 | 0.592 | |
| 4lxb | 7R9 | Prothrombin | 3.4.21.5 | 0.589 | |
| 1k22 | MEL | Prothrombin | 3.4.21.5 | 0.588 | |
| 2bxt | C2D | Prothrombin | 3.4.21.5 | 0.587 | |
| 2v3h | I25 | Prothrombin | 3.4.21.5 | 0.585 | |
| 1zgi | 382 | Prothrombin | 3.4.21.5 | 0.576 | |
| 1uma | IN2 | Prothrombin | 3.4.21.5 | 0.573 | |
| 4e7r | 0NW | Prothrombin | 3.4.21.5 | 0.573 | |
| 3utu | 1TS | Prothrombin | 3.4.21.5 | 0.572 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.571 | |
| 3qtv | 06P | Prothrombin | 3.4.21.5 | 0.571 | |
| 1gj5 | 130 | Prothrombin | 3.4.21.5 | 0.570 | |
| 4az2 | 9MU | Prothrombin | 3.4.21.5 | 0.561 | |
| 2gde | SN3 | Prothrombin | 3.4.21.5 | 0.560 | |
| 1o2g | 696 | Prothrombin | 3.4.21.5 | 0.555 | |
| 1o5g | CR9 | Prothrombin | 3.4.21.5 | 0.548 | |
| 1c1u | BAI | Prothrombin | 3.4.21.5 | 0.546 | |
| 3f68 | 91U | Prothrombin | 3.4.21.5 | 0.537 | |
| 2ziq | 26U | Prothrombin | 3.4.21.5 | 0.530 | |
| 1c5n | ESI | Prothrombin | 3.4.21.5 | 0.518 | |
| 5cmx | 0G6 | Prothrombin | 3.4.21.5 | 0.517 | |
| 1o0d | 163 | Prothrombin | 3.4.21.5 | 0.511 | |
| 1riw | OSC | Prothrombin | 3.4.21.5 | 0.511 | |
| 1c4v | IH2 | Prothrombin | 3.4.21.5 | 0.510 | |
| 4ayv | 9MQ | Prothrombin | 3.4.21.5 | 0.508 | |
| 1ta2 | 176 | Prothrombin | 3.4.21.5 | 0.489 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.488 | |
| 1ny2 | ARG_PRO_PRO_GLY | Prothrombin | 3.4.21.5 | 0.484 | |
| 3qdz | PRO_ALA_PRO_ARG | Prothrombin | 3.4.21.5 | 0.483 | |
| 3mau | PLR | Putative sphingosine-1-phosphate lyase | / | 0.478 | |
| 2ign | FAD | Pyranose 2-oxidase | / | 0.477 | |
| 1ju2 | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.476 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.476 | |
| 1j9z | FAD | NADPH--cytochrome P450 reductase | / | 0.473 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.473 | |
| 4loy | 6XS | Prothrombin | 3.4.21.5 | 0.472 | |
| 5c6c | CMP | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.470 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.469 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.469 | |
| 1mu8 | CDB | Prothrombin | 3.4.21.5 | 0.466 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.465 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.465 | |
| 2e7r | SAH | Diphthine synthase | / | 0.463 | |
| 2p5c | SAH | Diphthine synthase | / | 0.463 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.461 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.461 | |
| 1fml | RTL | Retinol dehydratase | / | 0.459 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.459 | |
| 3zks | WZV | Beta-secretase 2 | 3.4.23.45 | 0.456 | |
| 4jey | PLP | Acetylornithine/succinyldiaminopimelate aminotransferase | 2.6.1.11 | 0.456 | |
| 2hdj | NDP | Aldo-keto reductase family 1 member C2 | / | 0.455 | |
| 4b1j | A1R | Poly(ADP-ribose) glycohydrolase | 3.2.1.143 | 0.455 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.454 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.454 | |
| 2yk2 | YJX | Heat shock protein HSP 90-alpha | / | 0.454 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.454 | |
| 3nu0 | 3TU | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 3uxv | GUN | NADPH-dependent 7-cyano-7-deazaguanine reductase | / | 0.454 | |
| 3zw9 | NAD | Peroxisomal bifunctional enzyme | 1.1.1.35 | 0.454 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.453 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.452 | |
| 4gv0 | 8ME | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.452 | |
| 2pg0 | FAD | Acyl-CoA dehydrogenase | / | 0.451 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.451 | |
| 3eks | CY9 | Actin-5C | / | 0.451 | |
| 3eku | CY9 | Actin-5C | / | 0.451 | |
| 3mau | EXT | Putative sphingosine-1-phosphate lyase | / | 0.451 | |
| 4jtq | NAP | Aldo-keto reductase family 1 member C2 | / | 0.451 | |
| 1sa5 | BMV | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.450 | |
| 1qoq | IGP | Tryptophan synthase alpha chain | / | 0.449 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 3exf | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.448 | |
| 3exf | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.448 | |
| 4tvj | 09L | Poly [ADP-ribose] polymerase 2 | 2.4.2.30 | 0.448 | |
| 1gj4 | 132 | Prothrombin | 3.4.21.5 | 0.447 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.447 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.447 | |
| 2fhl | BNI | Avidin-related protein 4/5 | / | 0.447 | |
| 2pk3 | A2R | GDP-6-deoxy-D-mannose reductase | / | 0.447 | |
| 2zev | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.447 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.446 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 2xuh | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 3bg7 | FAD | Pyranose 2-oxidase | / | 0.445 | |
| 4ktk | KTK | Cytochrome P450 | / | 0.445 | |
| 1nl4 | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.444 | |
| 1s20 | NAD | 2,3-diketo-L-gulonate reductase | 1.1.1.130 | 0.444 | |
| 2p2x | SAH | Diphthine synthase | / | 0.444 | |
| 2yk2 | YJW | Heat shock protein HSP 90-alpha | / | 0.444 | |
| 3akz | GSU | Glutamate--tRNA ligase 2 | / | 0.444 | |
| 3h7r | NAP | Aldo-keto reductase family 4 member C8 | / | 0.444 | |
| 1c7o | PPG | Hemolysin | / | 0.443 | |
| 1nyt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.443 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.443 | |
| 2wu4 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.442 | |
| 2gyw | OBI | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 3ihz | FK5 | Peptidylprolyl isomerase | / | 0.442 | |
| 3phi | NDP | Shikimate dehydrogenase (NADP(+)) | / | 0.442 | |
| 3sqx | ANP | ATP-dependent RNA helicase MSS116, mitochondrial | 3.6.4.13 | 0.441 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 3vy2 | FMN | FMN-binding protein | / | 0.440 |