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 |
|---|---|---|---|
| 2wep | ADP | ATP-dependent molecular chaperone HSP82 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2wep | ADP | ATP-dependent molecular chaperone HSP82 | / | 1.000 | |
| 1am1 | ADP | ATP-dependent molecular chaperone HSP82 | / | 0.644 | |
| 3r4p | FU7 | Heat shock protein HSP 90-alpha | / | 0.606 | |
| 3r4n | FU5 | Heat shock protein HSP 90-alpha | / | 0.597 | |
| 4ce3 | L4V | ATP-dependent molecular chaperone HSP82 | / | 0.596 | |
| 2wer | RDC | ATP-dependent molecular chaperone HSP82 | / | 0.586 | |
| 3eko | PYU | Heat shock protein HSP 90-alpha | / | 0.580 | |
| 1u0z | RDC | Endoplasmin | / | 0.579 | |
| 3k98 | 1RC | Heat shock protein HSP 90-alpha | / | 0.579 | |
| 2iwu | NP5 | ATP-dependent molecular chaperone HSP82 | / | 0.577 | |
| 4bqj | XKL | Heat shock protein HSP 90-alpha | / | 0.577 | |
| 3rlq | 3RQ | Heat shock protein HSP 90-alpha | / | 0.576 | |
| 2vw5 | BC6 | ATP-dependent molecular chaperone HSP82 | / | 0.570 | |
| 3rlr | 3RR | Heat shock protein HSP 90-alpha | / | 0.567 | |
| 1ysz | NEC | Endoplasmin | / | 0.565 | |
| 4fcr | 0TM | Heat shock protein HSP 90-alpha | / | 0.559 | |
| 3hhu | 819 | Heat shock protein HSP 90-alpha | / | 0.555 | |
| 3hek | BD0 | Heat shock protein HSP 90-alpha | / | 0.554 | |
| 4xc0 | ACP | Heat shock cognate 90 kDa protein | / | 0.551 | |
| 3ekr | PY9 | Heat shock protein HSP 90-alpha | / | 0.550 | |
| 3k99 | PFT | Heat shock protein HSP 90-alpha | / | 0.546 | |
| 3t10 | ACP | Heat shock protein HSP 90-alpha | / | 0.543 | |
| 2gqp | PA7 | Endoplasmin | / | 0.540 | |
| 4as9 | 4QS | ATP-dependent molecular chaperone HSP82 | / | 0.536 | |
| 1u2o | NEC | Endoplasmin | / | 0.533 | |
| 1bgq | RDC | ATP-dependent molecular chaperone HSP82 | / | 0.531 | |
| 2bt0 | CT5 | Heat shock protein HSP 90-alpha | / | 0.529 | |
| 2hch | N5A | Endoplasmin | / | 0.526 | |
| 2yef | ANP | Heat shock protein HSP 90-alpha | / | 0.526 | |
| 1y4s | ADP | Chaperone protein HtpG | / | 0.525 | |
| 3k97 | 4CD | Heat shock protein HSP 90-alpha | / | 0.525 | |
| 2xht | C0Y | Heat shock protein HSP 90-alpha | / | 0.524 | |
| 2yeg | XQG | Heat shock protein HSP 90-alpha | / | 0.524 | |
| 2xab | VHD | Heat shock protein HSP 90-alpha | / | 0.523 | |
| 2byh | 2D7 | Heat shock protein HSP 90-alpha | / | 0.520 | |
| 2fyp | RDE | Endoplasmin | / | 0.519 | |
| 1qy8 | RDI | Endoplasmin | / | 0.517 | |
| 2xd6 | XD6 | ATP-dependent molecular chaperone HSP82 | / | 0.517 | |
| 4gqt | ADP | Heat shock protein 90 | / | 0.516 | |
| 2bre | KJ2 | ATP-dependent molecular chaperone HSP82 | / | 0.514 | |
| 4ce1 | 7FK | ATP-dependent molecular chaperone HSP82 | / | 0.513 | |
| 1byq | ADP | Heat shock protein HSP 90-alpha | / | 0.510 | |
| 2wi6 | ZZ6 | Heat shock protein HSP 90-alpha | / | 0.510 | |
| 2xk2 | ADP | Heat shock protein HSP 90-alpha | / | 0.510 | |
| 2brc | CT5 | ATP-dependent molecular chaperone HSP82 | / | 0.508 | |
| 5f5r | ANP | Heat shock protein 75 kDa, mitochondrial | / | 0.508 | |
| 1u0y | PA7 | Endoplasmin | / | 0.506 | |
| 2byi | 2DD | Heat shock protein HSP 90-alpha | / | 0.506 | |
| 2gfd | RDA | Endoplasmin | / | 0.505 | |
| 3t2s | AGS | Heat shock protein HSP 90-alpha | / | 0.502 | |
| 1yc3 | 4BC | Heat shock protein HSP 90-alpha | / | 0.501 | |
| 1uy8 | PU5 | Heat shock protein HSP 90-alpha | / | 0.500 | |
| 2q8i | RDC | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 3, mitochondrial | 2.7.11.2 | 0.498 | |
| 1uyf | PU1 | Heat shock protein HSP 90-alpha | / | 0.497 | |
| 3c11 | GDM | ATP-dependent molecular chaperone HSP82 | / | 0.497 | |
| 1qy5 | NEC | Endoplasmin | / | 0.496 | |
| 1uyd | PU8 | Heat shock protein HSP 90-alpha | / | 0.496 | |
| 4asg | 814 | ATP-dependent molecular chaperone HSP82 | / | 0.496 | |
| 2bz5 | AB4 | Heat shock protein HSP 90-alpha | / | 0.495 | |
| 3b28 | B2X | Heat shock protein HSP 90-alpha | / | 0.495 | |
| 2iwx | M1S | ATP-dependent molecular chaperone HSP82 | / | 0.494 | |
| 4xcj | ADP | Heat shock cognate 90 kDa protein | / | 0.494 | |
| 3r4o | FU3 | Heat shock protein HSP 90-alpha | / | 0.491 | |
| 3vha | VHA | Heat shock protein HSP 90-alpha | / | 0.491 | |
| 4ce2 | BO5 | ATP-dependent molecular chaperone HSP82 | / | 0.489 | |
| 2yi5 | YI5 | Heat shock protein HSP 90-alpha | / | 0.488 | |
| 1uy7 | PU4 | Heat shock protein HSP 90-alpha | / | 0.487 | |
| 2hg1 | N5O | Endoplasmin | / | 0.486 | |
| 2yee | 2EC | Heat shock protein HSP 90-alpha | / | 0.486 | |
| 4egi | B2J | Heat shock protein HSP 90-alpha | / | 0.485 | |
| 2xx2 | 13C | ATP-dependent molecular chaperone HSP82 | / | 0.484 | |
| 2xhr | C0P | Heat shock protein HSP 90-alpha | / | 0.481 | |
| 2ykj | YKJ | Heat shock protein HSP 90-alpha | / | 0.480 | |
| 4nh8 | 2LC | Heat shock protein HSP 90-alpha | / | 0.480 | |
| 1uym | PU3 | Heat shock protein HSP 90-beta | / | 0.477 | |
| 2yjx | YJX | Heat shock protein HSP 90-alpha | / | 0.477 | |
| 4efu | EFU | Heat shock protein HSP 90-alpha | / | 0.477 | |
| 1diu | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.476 | |
| 2yki | YKI | Heat shock protein HSP 90-alpha | / | 0.474 | |
| 2wi7 | 2KL | Heat shock protein HSP 90-alpha | / | 0.473 | |
| 4jql | VJ6 | Heat shock protein HSP 90-alpha | / | 0.473 | |
| 2qfo | A13 | Heat shock protein HSP 90-alpha | / | 0.472 | |
| 3hz5 | Z64 | Heat shock protein HSP 90-alpha | / | 0.471 | |
| 2xcm | ADP | Cytosolic heat shock protein 90 | / | 0.470 | |
| 4bqg | 50Q | Heat shock protein HSP 90-alpha | / | 0.469 | |
| 1amw | ADP | ATP-dependent molecular chaperone HSP82 | / | 0.468 | |
| 4xcl | AGS | Heat shock cognate 90 kDa protein | / | 0.468 | |
| 1lf3 | EH5 | Plasmepsin-2 | 3.4.23.39 | 0.467 | |
| 2fwy | H64 | Heat shock protein HSP 90-alpha | / | 0.466 | |
| 1uy9 | PU6 | Heat shock protein HSP 90-alpha | / | 0.463 | |
| 3inx | JZC | Heat shock protein HSP 90-alpha | / | 0.463 | |
| 3wha | WHA | Heat shock protein HSP 90-alpha | / | 0.463 | |
| 3hyz | 42C | Heat shock protein HSP 90-alpha | / | 0.462 | |
| 3inw | JZB | Heat shock protein HSP 90-alpha | / | 0.462 | |
| 3t1k | ANP | Heat shock protein HSP 90-alpha | / | 0.462 | |
| 4bii | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.462 | |
| 1uyh | PU0 | Heat shock protein HSP 90-alpha | / | 0.461 | |
| 2h55 | DZ8 | Heat shock protein HSP 90-alpha | / | 0.461 | |
| 3hz1 | 42C | Heat shock protein HSP 90-alpha | / | 0.461 | |
| 3hz1 | 37D | Heat shock protein HSP 90-alpha | / | 0.461 | |
| 4hy6 | FJ1 | Heat shock protein HSP 90-alpha | / | 0.461 | |
| 1dhr | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.460 | |
| 2qhy | MZ1 | Gag-Pol polyprotein | / | 0.460 | |
| 3ied | AN2 | HSP90 | / | 0.460 | |
| 4asf | 62U | ATP-dependent molecular chaperone HSP82 | / | 0.460 | |
| 4dh6 | 0KN | Beta-secretase 1 | 3.4.23.46 | 0.460 | |
| 3d0b | SNX | Heat shock protein HSP 90-alpha | / | 0.459 | |
| 4eft | EFT | Heat shock protein HSP 90-alpha | / | 0.459 | |
| 2qi3 | MZ5 | Gag-Pol polyprotein | / | 0.458 | |
| 2yk2 | YJX | Heat shock protein HSP 90-alpha | / | 0.458 | |
| 2znq | 401 | Peroxisome proliferator-activated receptor delta | / | 0.458 | |
| 3sa5 | A69 | Protease | / | 0.458 | |
| 3ogq | AB1 | Pol polyprotein | / | 0.457 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.457 | |
| 2fde | 385 | Gag-Pol polyprotein | 3.4.23.16 | 0.456 | |
| 3i2l | 2NC | Protease | / | 0.456 | |
| 1uyc | PU7 | Heat shock protein HSP 90-alpha | / | 0.455 | |
| 2iws | NP4 | ATP-dependent molecular chaperone HSP82 | / | 0.455 | |
| 2yke | YKE | Heat shock protein HSP 90-alpha | / | 0.455 | |
| 3o6o | 94M | Heat shock protein 83 | / | 0.455 | |
| 3lzu | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.454 | |
| 2p33 | J07 | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.453 | |
| 2qhc | AB1 | Protease | / | 0.453 | |
| 3ndt | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.453 | |
| 3zw9 | NAD | Peroxisomal bifunctional enzyme | 1.1.1.35 | 0.453 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.453 | |
| 2rkf | AB1 | Pol protein | / | 0.452 | |
| 2yk2 | YJW | Heat shock protein HSP 90-alpha | / | 0.452 | |
| 3ec0 | GRL | Gag-Pol polyprotein | 3.4.23.47 | 0.452 | |
| 3kdd | JZQ | Gag-Pol polyprotein | 3.4.23.16 | 0.452 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 2vwc | BC2 | ATP-dependent molecular chaperone HSP82 | / | 0.451 | |
| 3djk | G55 | Gag-Pol polyprotein | 3.4.23.16 | 0.451 | |
| 3o0i | P54 | Heat shock protein HSP 90-alpha | / | 0.451 | |
| 4njs | G08 | Protease | / | 0.451 | |
| 4r8q | ADP | Mitotic checkpoint serine/threonine-protein kinase BUB1 | 2.7.11.1 | 0.451 | |
| 1nhh | ANP | DNA mismatch repair protein MutL | / | 0.450 | |
| 1uye | PU9 | Heat shock protein HSP 90-alpha | / | 0.450 | |
| 1xny | 191 | Propionyl-CoA carboxylase complex B subunit | / | 0.450 | |
| 2b4t | AES | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.450 | |
| 2cgf | P2N | ATP-dependent molecular chaperone HSP82 | / | 0.450 | |
| 2q9f | C3S | Cholesterol 24-hydroxylase | / | 0.450 | |
| 2qg2 | A91 | Heat shock protein HSP 90-alpha | / | 0.450 | |
| 2xx4 | 13I | ATP-dependent molecular chaperone HSP82 | / | 0.450 | |
| 2z3u | CRR | Cytochrome P450 | / | 0.450 | |
| 3crl | ANP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial | 2.7.11.2 | 0.450 | |
| 4bcr | WY1 | Peroxisome proliferator-activated receptor alpha | / | 0.450 | |
| 1hxw | RIT | Gag-Pol polyprotein | / | 0.449 | |
| 2ykb | YKB | Heat shock protein HSP 90-alpha | / | 0.449 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.449 | |
| 3cyw | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.449 | |
| 3so9 | 017 | Pol protein | / | 0.449 | |
| 3upj | U03 | Gag-Pol polyprotein | / | 0.449 | |
| 4hla | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.449 | |
| 3o9c | K20 | Pol polyprotein | / | 0.448 | |
| 2bu8 | ADP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial | 2.7.11.2 | 0.447 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.447 | |
| 3o9i | A61 | Gag-Pol polyprotein | / | 0.447 | |
| 3vf5 | 031 | Gag-Pol polyprotein | 3.4.23.16 | 0.447 | |
| 4bgi | I4I | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.447 | |
| 4f65 | 0S9 | Fibroblast growth factor receptor 1 | / | 0.447 | |
| 2fxs | RDA | ATP-dependent molecular chaperone HSP82 | / | 0.446 | |
| 2gr1 | FAD | Ferredoxin reductase | / | 0.446 | |
| 2yei | XQI | Heat shock protein HSP 90-alpha | / | 0.446 | |
| 3ekt | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 3ekw | DR7 | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 3kb1 | ADP | Iron-sulfur cluster carrier protein | / | 0.446 | |
| 4hdb | G52 | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.446 | |
| 4ye3 | G04 | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 1dir | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.445 | |
| 1w4z | NAP | Putative ketoacyl reductase | 1.3.1 | 0.445 | |
| 3el4 | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.445 | |
| 3oez | STI | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.445 | |
| 3oxv | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.445 | |
| 3qp0 | NI8 | Gag-Pol polyprotein | 3.4.23.16 | 0.445 | |
| 4a6b | QG8 | Gag-Pol polyprotein | 3.4.23.16 | 0.445 | |
| 4dqe | 017 | Gag-Pol polyprotein | / | 0.445 | |
| 4enh | FVX | Cholesterol 24-hydroxylase | / | 0.445 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.444 | |
| 2fwz | H71 | Heat shock protein HSP 90-alpha | / | 0.444 | |
| 2psv | MUV | Protease | / | 0.444 | |
| 2vyn | NAD | Glyceraldehyde-3-phosphate dehydrogenase A | / | 0.444 | |
| 2w9s | TOP | Dihydrofolate reductase type 1 from Tn4003 | 1.5.1.3 | 0.444 | |
| 3bva | 2NC | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 3mnr | SD1 | Heat shock protein HSP 90-alpha | / | 0.444 | |
| 4djr | 0KJ | Pol polyprotein | / | 0.444 | |
| 4dqh | 017 | Gag-Pol polyprotein | / | 0.444 | |
| 3jvw | DMP | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 3mxd | K53 | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.443 | |
| 3sa9 | A68 | Protease | / | 0.443 | |
| 1bvr | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.442 | |
| 1dhj | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1fg6 | 2NC | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 1qnf | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.442 | |
| 1uyi | PUZ | Heat shock protein HSP 90-alpha | / | 0.442 | |
| 2f3k | RO1 | Protease | / | 0.442 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.442 | |
| 3ad9 | NAD | Subunit alpha of sarocosine oxidase | / | 0.442 | |
| 3i7e | DJR | Gag-Pol polyprotein | / | 0.442 | |
| 4djo | MK5 | Pol polyprotein | / | 0.442 | |
| 4heg | G52 | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 4r20 | AER | Cytochrome P450 family 17 polypeptide 2 | / | 0.442 | |
| 1ec3 | MS3 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.441 | |
| 2b60 | RIT | Pol polyprotein | / | 0.441 | |
| 2bpv | 1IN | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.441 | |
| 2qi7 | MZ9 | Gag-Pol polyprotein | / | 0.441 | |
| 2znn | S44 | Peroxisome proliferator-activated receptor alpha | / | 0.441 | |
| 3ict | ADP | Coenzyme A disulfide reductase | / | 0.441 | |
| 3o9a | K14 | Pol polyprotein | / | 0.441 | |
| 4bid | IE8 | Mitogen-activated protein kinase kinase kinase 5 | 2.7.11.25 | 0.441 | |
| 4hbg | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.441 | |
| 4i8z | G08 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 4qgi | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 1mes | DMP | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 1t7j | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 1wbm | BLL | Pol protein | / | 0.440 | |
| 1z1r | HBH | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 2e8u | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.440 | |
| 3jw2 | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 7upj | INU | Gag-Pol polyprotein | 3.4.23.16 | 0.440 |