3BZ3 - chain A (model A) | Protein tyrosine kinase 2
Structure information
| PDB: | 3BZ3 |
| PubMed: | 18339875 |
| Release date: | 2008-04-01 |
| Resolution: | 2.2 Å |
| Kinase: | PTK2 (FAK) |
| Family: | FAK |
| Group: | TK |
| Species: | HUMAN |
| Quality Score: | 8 |
| Missing Residues: | 0 |
| Missing Atoms: | 0 |
| DFG conformation: | in |
| αC-helix conformation: | in |
| Salt bridge KIII.17 and EαC.24: | Yes (2.6Å) |
| ASP rotation (xDFG.81) : | 59° |
| PHE rotation (xDFG.82) : | 13° |
| Activation loop position: | -3.6Å |
| αC-helix position: | 18.5Å |
| G-rich loop angle: | 64.9° |
| G-rich loop distance: | 19.1Å |
| G-rich loop rotation: | 93.4° |
Other models from this PDB:
2D & 3D views
Binding pocket waters
The following waters were found in the defined clusters:
I1
H-bond protein
Binding pocket sequence
| Uniprot | RCIGEGQFGDVHQVAIKTCKFLQEALTMRQFDPHIVKLIGVWIIMELCTLGELRSFLQVYLESKRFVHRDIAARNVLVLGDFGLS |
| Structure: | RCIGEGQFGDVHQVAIKTCKFLQEALTMRQFDPHIVKLIGVWIIMELCTLGELRSFLQVYLESKRFVHRDIAARNVLVLGDFGLS |
Modified residues
No modified residues identified.
Orthosteric ligand
Ligand HET-code: YAM
Ligand Name: N-methyl-N-{3-[({2-[(2-oxo-2,3-dihydro-1H-indol-5-yl)amino]-5-(trifluoromethyl)pyrimidin-4-yl}amino)methyl]pyridin-2-yl}methanesulfonamide
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- LABELS
- KLIFS residue #
- Amino Acid
- None
- COLORS
- Interaction types
- KLIFS (all res.)
- KLIFS (interacting res.)
- None
- OTHER
- Show/hide non-interacting res.
- En/disable resizing interacting res.
This ligand targets the following (sub)pockets:
| Main pockets | |
|---|---|
| Front | |
| Gate | |
| Back | |
| Subpockets | |
|---|---|
| FP-I | |
| FP-II | |
| BP-I-A | |
| BP-I-B | |
| BP-II-in | |
| BP-II-A-in | |
| BP-II-B-in | |
| BP-II-out | |
| BP-II-B | |
| BP-III | |
| BP-IV | |
| BP-V | |
Kinase-ligand interactions
■ Hydrophobic ♦ Aromatic face-to-face ♦ Aromatic face-to-edge ▲ H-bond donor ▲ H-bond acceptor ● Ionic positive ● Ionic negative
| I | g.l | II | III | αC | |||||||||||||||
| 1 R 426 | 2 C 427 | 3 I 428 | 4 G 429 | 5 E 430 | 6 G 431 | 7 Q 432 | 8 F 433 | 9 G 434 | 10 D 435 | 11 V 436 | 12 H 437 | 13 Q 438 | 14 V 451 | 15 A 452 | 16 I 453 | 17 K 454 | 18 T 455 | 19 C 456 | 20 K 467 |
| ■▲ | ■ | ■ | ■ | ■ | ■ | ■ | |||||||||||||
| αC | b.l | IV | |||||||||||||||||
| 21 F 468 | 22 L 469 | 23 Q 470 | 24 E 471 | 25 A 472 | 26 L 473 | 27 T 474 | 28 M 475 | 29 R 476 | 30 Q 477 | 31 F 478 | 32 D 479 | 33 P 481 | 34 H 482 | 35 I 483 | 36 V 484 | 37 K 485 | 38 L 486 | 39 I 487 | 40 G 488 |
| ■ | |||||||||||||||||||
| IV | V | GK | hinge | linker | αD | αE | |||||||||||||
| 41 V 489 | 42 W 496 | 43 I 497 | 44 I 498 | 45 M 499 | 46 E 500 | 47 L 501 | 48 C 502 | 49 T 503 | 50 L 504 | 51 G 505 | 52 E 506 | 53 L 507 | 54 R 508 | 55 S 509 | 56 F 510 | 57 L 511 | 58 Q 512 | 59 V 513 | 60 Y 536 |
| ■ | ■ | ■ | ■▲▲ | ■ | ■ | ■ | |||||||||||||
| αE | VI | c.l | VII | VIII | x | ||||||||||||||
| 61 L 537 | 62 E 538 | 63 S 539 | 64 K 540 | 65 R 541 | 66 F 542 | 67 V 543 | 68 H 544 | 69 R 545 | 70 D 546 | 71 I 547 | 72 A 548 | 73 A 549 | 74 R 550 | 75 N 551 | 76 V 552 | 77 L 553 | 78 V 554 | 79 L 562 | 80 G 563 |
| ■ | ■ | ■ | ■ | ||||||||||||||||
| DFG | a.l | ||||||||||||||||||
| 81 D 564 | 82 F 565 | 83 G 566 | 84 L 567 | 85 S 568 | |||||||||||||||
| ■ | ■ | ■ | |||||||||||||||||
Binding affinities
ChEMBL ID:CHEMBL1084546Bioaffinities: 162 records for 122 kinase(s)
| Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
|---|---|---|---|---|---|---|
| Homo sapiens | 3-phosphoinositide dependent protein kinase-1 | 6 | 6 | 6 | pKi | 1 |
| Homo sapiens | ALK tyrosine kinase receptor | 6.7 | 6.7 | 6.7 | pKi | 1 |
| Homo sapiens | AMP-activated protein kinase, alpha-1 subunit | 6.4 | 6.4 | 6.4 | pKi | 1 |
| Homo sapiens | BMP-2-inducible protein kinase | 5.5 | 5.5 | 5.5 | pKd | 1 |
| Homo sapiens | BR serine/threonine-protein kinase 1 | 5.3 | 5.3 | 5.3 | pKi | 1 |
| Homo sapiens | CaM kinase II delta | 5.4 | 5.4 | 5.4 | pKi | 1 |
| Homo sapiens | CaM kinase II gamma | 5.6 | 5.6 | 5.6 | pKi | 1 |
| Homo sapiens | CaM-kinase kinase beta | 6.5 | 6.5 | 6.5 | pKi | 1 |
| Homo sapiens | cAMP-dependent protein kinase alpha-catalytic subunit | 6.8 | 6.8 | 6.8 | pKi | 1 |
| Homo sapiens | Casein kinase I gamma 1 | 5.4 | 5.4 | 5.4 | pKi | 1 |
| Homo sapiens | Casein kinase I gamma 2 | 5.8 | 5.8 | 5.8 | pKd | 1 |
| Homo sapiens | Casein kinase I gamma 2 | 5.4 | 5.4 | 5.4 | pKi | 1 |
| Homo sapiens | Casein kinase II alpha | 6 | 6 | 6 | pKi | 1 |
| Homo sapiens | Casein kinase II alpha (prime) | 6 | 6 | 6 | pKd | 1 |
| Homo sapiens | c-Jun N-terminal kinase 2 | 5.8 | 5.8 | 5.8 | pKi | 1 |
| Homo sapiens | c-Jun N-terminal kinase 3 | 6.6 | 6.6 | 6.6 | pKi | 1 |
| Homo sapiens | Cyclin-dependent kinase 1 | 5.8 | 5.8 | 5.8 | pKd | 1 |
| Homo sapiens | Cyclin-dependent kinase 1 | 7.2 | 7.2 | 7.2 | pKi | 1 |
| Homo sapiens | Cyclin-dependent kinase 13 | 5.4 | 5.4 | 5.4 | pKd | 1 |
| Homo sapiens | Cyclin-dependent kinase 2 | 6 | 6 | 6 | pKd | 1 |
| Homo sapiens | Cyclin-dependent kinase 2 | 7.1 | 7.1 | 7.1 | pKi | 1 |
| Homo sapiens | Cyclin-dependent kinase 3 | 5.5 | 5.5 | 5.5 | pKd | 1 |
| Homo sapiens | Cyclin-dependent kinase 5 | 6.3 | 6.3 | 6.3 | pKd | 1 |
| Homo sapiens | Cyclin-dependent kinase 5 | 7.8 | 7.8 | 7.8 | pKi | 1 |
| Homo sapiens | Cyclin-dependent kinase 7 | 5.9 | 5.9 | 5.9 | pKd | 1 |
| Homo sapiens | Cyclin-dependent kinase 7 | 7.7 | 7.7 | 7.7 | pKi | 1 |
| Homo sapiens | Cyclin-dependent kinase 9 | 5.9 | 5.9 | 5.9 | pKd | 1 |
| Homo sapiens | Cyclin-dependent kinase 9 | 7.2 | 7.2 | 7.2 | pKi | 1 |
| Homo sapiens | Death-associated protein kinase 3 | 6 | 6 | 6 | pKi | 1 |
| Homo sapiens | Dual specificity mitogen-activated protein kinase kinase 2 | 5.6 | 5.6 | 5.6 | pKi | 1 |
| Homo sapiens | Dual specificity mitogen-activated protein kinase kinase 6 | 5.7 | 5.7 | 5.7 | pKd | 1 |
| Homo sapiens | Dual specificity protein kinase CLK2 | 6.9 | 6.9 | 6.9 | pKi | 1 |
| Homo sapiens | Dual specificity protein kinase CLK4 | 7.2 | 7.2 | 7.2 | pKi | 1 |
| Homo sapiens | Dual specificty protein kinase CLK1 | 6.4 | 6.4 | 6.4 | pKd | 1 |
| Homo sapiens | Ephrin type-A receptor 2 | 5.9 | 5.9 | 5.9 | pKi | 1 |
| Homo sapiens | Fibroblast growth factor receptor 1 | 6.2 | 6.2 | 6.2 | pKi | 1 |
| Homo sapiens | Fibroblast growth factor receptor 3 | 6.2 | 6.2 | 6.2 | pKi | 1 |
| Homo sapiens | Focal adhesion kinase 1 | 8.8 | 8.8 | 9 | pIC50 | 6 |
| Homo sapiens | Focal adhesion kinase 1 | 9 | 9 | 9 | pKd | 1 |
| Homo sapiens | Focal adhesion kinase 1 | 9.2 | 9.2 | 9.2 | pKi | 1 |
| Homo sapiens | Glycogen synthase kinase-3 alpha | 6.1 | 6.1 | 6.1 | pKd | 1 |
| Homo sapiens | Glycogen synthase kinase-3 alpha | 7.1 | 7.1 | 7.1 | pKi | 1 |
| Homo sapiens | Glycogen synthase kinase-3 beta | 6.2 | 6.2 | 6.2 | pKd | 1 |
| Homo sapiens | Glycogen synthase kinase-3 beta | 7 | 7 | 7 | pKi | 1 |
| Homo sapiens | G protein-coupled receptor kinase 5 | 5.6 | 5.6 | 5.6 | pKi | 1 |
| Homo sapiens | Hepatocyte growth factor receptor | 5.7 | 5.7 | 5.7 | pKd | 1 |
| Homo sapiens | Hepatocyte growth factor receptor | 6.6 | 6.6 | 6.6 | pKi | 1 |
| Homo sapiens | Homeodomain-interacting protein kinase 2 | 6.7 | 6.7 | 6.7 | pKi | 1 |
| Homo sapiens | Homeodomain-interacting protein kinase 4 | 6.3 | 6.3 | 6.3 | pKi | 1 |
| Homo sapiens | Insulin-like growth factor I receptor | 6.1 | 6.1 | 6.1 | pKi | 1 |
| Homo sapiens | Insulin receptor | 6.3 | 6.3 | 6.3 | pKi | 1 |
| Homo sapiens | Interleukin-1 receptor-associated kinase 1 | 5.7 | 5.7 | 5.7 | pKi | 1 |
| Homo sapiens | Interleukin-1 receptor-associated kinase 4 | 5.6 | 5.6 | 5.6 | pKd | 1 |
| Homo sapiens | Interleukin-1 receptor-associated kinase 4 | 6.4 | 6.4 | 6.4 | pKi | 1 |
| Homo sapiens | Leucine-rich repeat serine/threonine-protein kinase 2 | 6.8 | 6.8 | 6.8 | pKi | 1 |
| Homo sapiens | Leukocyte tyrosine kinase receptor | 6.5 | 6.5 | 6.5 | pKi | 1 |
| Homo sapiens | Macrophage-stimulating protein receptor | 6.6 | 6.6 | 6.6 | pKi | 1 |
| Homo sapiens | MAP kinase ERK2 | 5.9 | 5.9 | 5.9 | pKd | 1 |
| Homo sapiens | MAP kinase ERK2 | 7.2 | 7.2 | 7.2 | pKi | 1 |
| Homo sapiens | MAP kinase p38 gamma | 5.6 | 5.6 | 5.6 | pKi | 1 |
| Homo sapiens | MAP/microtubule affinity-regulating kinase 2 | 5.6 | 5.6 | 5.6 | pKd | 1 |
| Homo sapiens | MAP/microtubule affinity-regulating kinase 2 | 6.5 | 6.5 | 6.5 | pKi | 1 |
| Homo sapiens | MAP/microtubule affinity-regulating kinase 4 | 6.9 | 6.9 | 6.9 | pKd | 1 |
| Homo sapiens | MAP/microtubule affinity-regulating kinase 4 | 7.3 | 7.3 | 7.3 | pKi | 1 |
| Homo sapiens | Maternal embryonic leucine zipper kinase | 5.8 | 5.8 | 5.8 | pKd | 1 |
| Homo sapiens | Maternal embryonic leucine zipper kinase | 7.1 | 7.1 | 7.1 | pKi | 1 |
| Homo sapiens | Misshapen-like kinase 1 | 6.2 | 6.2 | 6.2 | pKi | 1 |
| Homo sapiens | Mitogen-activated protein kinase 15 | 5.8 | 5.8 | 5.8 | pKd | 1 |
| Homo sapiens | Mitogen-activated protein kinase 7 | 5.5 | 5.5 | 5.5 | pKd | 1 |
| Homo sapiens | Mitogen-activated protein kinase kinase kinase 10 | 6.7 | 6.7 | 6.7 | pKi | 1 |
| Homo sapiens | Mitogen-activated protein kinase kinase kinase 11 | 6.4 | 6.4 | 6.4 | pKd | 1 |
| Homo sapiens | Mitogen-activated protein kinase kinase kinase kinase 1 | 5.4 | 5.4 | 5.4 | pKd | 1 |
| Homo sapiens | Mitogen-activated protein kinase kinase kinase kinase 2 | 5.8 | 5.8 | 5.8 | pKi | 1 |
| Homo sapiens | Mitogen-activated protein kinase kinase kinase kinase 4 | 6.6 | 6.6 | 6.6 | pKd | 1 |
| Homo sapiens | Mitogen-activated protein kinase kinase kinase kinase 4 | 6.2 | 6.2 | 6.2 | pKi | 1 |
| Homo sapiens | Mitogen-activated protein kinase kinase kinase kinase 5 | 6.9 | 6.9 | 6.9 | pKi | 1 |
| Homo sapiens | Mixed lineage kinase 7 | 5.3 | 5.3 | 5.3 | pKi | 1 |
| Homo sapiens | Nerve growth factor receptor Trk-A | 6.4 | 6.4 | 6.4 | pKi | 1 |
| Homo sapiens | Neurotrophic tyrosine kinase receptor type 2 | 7.4 | 7.4 | 7.4 | pKi | 1 |
| Homo sapiens | Platelet-derived growth factor receptor beta | 6 | 6 | 6 | pKi | 1 |
| Homo sapiens | Protein kinase C delta | 4.9 | 4.9 | 4.9 | pKd | 1 |
| Homo sapiens | Protein kinase C delta | 5.8 | 5.8 | 5.8 | pKi | 1 |
| Homo sapiens | Protein kinase C gamma | 5.2 | 5.2 | 5.2 | pKi | 1 |
| Homo sapiens | Protein kinase C nu | 5.9 | 5.9 | 5.9 | pKi | 1 |
| Homo sapiens | Protein kinase C theta | 9 | 9 | 9 | pKd | 1 |
| Homo sapiens | Protein kinase C theta | 6.4 | 6.4 | 6.4 | pKi | 1 |
| Homo sapiens | Protein kinase N1 | 5.1 | 5.1 | 5.1 | pKd | 1 |
| Homo sapiens | Protein kinase N2 | 6.1 | 6.1 | 6.1 | pKi | 1 |
| Homo sapiens | Protein tyrosine kinase 2 beta | 7.9 | 7.9 | 7.9 | pIC50 | 3 |
| Homo sapiens | Protein tyrosine kinase 2 beta | 7.1 | 7.1 | 7.1 | pKd | 1 |
| Homo sapiens | Protein tyrosine kinase 2 beta | 8.5 | 8.5 | 8.5 | pKi | 1 |
| Homo sapiens | Proto-oncogene tyrosine-protein kinase ROS | 7.9 | 7.9 | 7.9 | pKi | 1 |
| Homo sapiens | Rho-associated protein kinase 1 | 5.7 | 5.7 | 5.7 | pKi | 1 |
| Homo sapiens | Rho-associated protein kinase 2 | 5.7 | 5.7 | 5.7 | pKi | 1 |
| Homo sapiens | Ribosomal protein S6 kinase 1 | 5.5 | 5.5 | 5.5 | pKi | 1 |
| Homo sapiens | Ribosomal protein S6 kinase alpha 3 | 6.3 | 6.3 | 6.3 | pKi | 2 |
| Homo sapiens | Serine/threonine-protein kinase 11 | 6.2 | 6.2 | 6.2 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase 16 | 6.9 | 6.9 | 6.9 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase 17A | 5.9 | 5.9 | 5.9 | pKi | 1 |
| Homo sapiens | Serine/threonine-protein kinase 2 | 5.1 | 5.1 | 5.1 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase 2 | 6.6 | 6.6 | 6.6 | pKi | 1 |
| Homo sapiens | Serine/threonine-protein kinase Aurora-A | 6.2 | 6.2 | 6.2 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase Aurora-A | 6.9 | 6.9 | 6.9 | pKi | 1 |
| Homo sapiens | Serine/threonine-protein kinase Aurora-B | 6 | 6 | 6 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase Aurora-B | 7.2 | 7.2 | 7.2 | pKi | 1 |
| Homo sapiens | Serine/threonine-protein kinase Chk2 | 6.1 | 6.1 | 6.1 | pKi | 1 |
| Homo sapiens | Serine/threonine-protein kinase c-TAK1 | 5.6 | 5.6 | 5.6 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase c-TAK1 | 6.7 | 6.7 | 6.7 | pKi | 1 |
| Homo sapiens | Serine/threonine-protein kinase D2 | 5.7 | 5.7 | 5.7 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase D2 | 5.9 | 5.9 | 5.9 | pKi | 1 |
| Homo sapiens | Serine/threonine-protein kinase MRCK-A | 5.2 | 5.2 | 5.2 | pKi | 1 |
| Homo sapiens | Serine/threonine-protein kinase MST1 | 5.2 | 5.2 | 5.2 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase MST2 | 5.6 | 5.6 | 5.6 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase MST2 | 6.3 | 6.3 | 6.3 | pKi | 1 |
| Homo sapiens | Serine/threonine-protein kinase MST4 | 7.9 | 7.9 | 7.9 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase PAK 1 | 5.4 | 5.4 | 5.4 | pKi | 1 |
| Homo sapiens | Serine/threonine-protein kinase PAK 4 | 5.9 | 5.9 | 5.9 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase PAK 4 | 6.7 | 6.7 | 6.7 | pKi | 1 |
| Homo sapiens | Serine/threonine-protein kinase PCTAIRE-1 | 5.7 | 5.7 | 5.7 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase PCTAIRE-2 | 7.1 | 7.1 | 7.1 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase PLK4 | 6.2 | 6.2 | 6.2 | pKi | 1 |
| Homo sapiens | Serine/threonine-protein kinase PRKX | 6.1 | 6.1 | 6.1 | pKi | 1 |
| Homo sapiens | Serine/threonine-protein kinase Sgk2 | 5.6 | 5.6 | 5.6 | pKi | 1 |
| Homo sapiens | Serine/threonine-protein kinase SIK2 | 6.7 | 6.7 | 6.7 | pKi | 1 |
| Homo sapiens | Serine/threonine-protein kinase SRPK1 | 5.8 | 5.8 | 5.8 | pKi | 1 |
| Homo sapiens | Serine/threonine-protein kinase TAO1 | 6.7 | 6.7 | 6.7 | pKi | 1 |
| Homo sapiens | Serine/threonine-protein kinase TAO3 | 4.9 | 4.9 | 4.9 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase TBK1 | 5.7 | 5.7 | 5.7 | pKi | 1 |
| Homo sapiens | Testis-specific serine/threonine-protein kinase 1 | 5.8 | 5.8 | 5.8 | pKi | 1 |
| Homo sapiens | Tyrosine kinase non-receptor protein 2 | 5.9 | 5.9 | 5.9 | pKi | 1 |
| Homo sapiens | Tyrosine-protein kinase BLK | 6.4 | 6.4 | 6.4 | pKi | 1 |
| Homo sapiens | Tyrosine-protein kinase BTK | 5.7 | 5.7 | 5.7 | pKi | 1 |
| Homo sapiens | Tyrosine-protein kinase CTK | 7 | 7 | 7 | pKi | 1 |
| Homo sapiens | Tyrosine-protein kinase FER | 6.1 | 6.1 | 6.1 | pKd | 1 |
| Homo sapiens | Tyrosine-protein kinase FRK | 7.4 | 7.4 | 7.4 | pKi | 1 |
| Homo sapiens | Tyrosine-protein kinase FYN | 5.7 | 5.7 | 5.7 | pKi | 1 |
| Homo sapiens | Tyrosine-protein kinase HCK | 5.5 | 5.5 | 5.5 | pKi | 1 |
| Homo sapiens | Tyrosine-protein kinase ITK/TSK | 7.1 | 7.1 | 7.1 | pKi | 1 |
| Homo sapiens | Tyrosine-protein kinase JAK2 | 7.1 | 7.1 | 7.1 | pKi | 2 |
| Homo sapiens | Tyrosine-protein kinase JAK3 | 6 | 6 | 6 | pKi | 2 |
| Homo sapiens | Tyrosine-protein kinase LCK | 6.3 | 6.3 | 6.3 | pKi | 1 |
| Homo sapiens | Tyrosine-protein kinase Lyn | 7 | 7 | 7 | pKi | 1 |
| Homo sapiens | Tyrosine-protein kinase receptor FLT3 | 5.9 | 5.9 | 5.9 | pKd | 1 |
| Homo sapiens | Tyrosine-protein kinase receptor FLT3 | 6.4 | 6.4 | 6.4 | pKi | 1 |
| Homo sapiens | Tyrosine-protein kinase receptor RET | 6.5 | 6.5 | 6.5 | pKi | 1 |
| Homo sapiens | Tyrosine-protein kinase receptor UFO | 6.7 | 6.7 | 6.7 | pKi | 1 |
| Homo sapiens | Tyrosine-protein kinase SRC | 6.3 | 6.3 | 6.3 | pKi | 1 |
| Homo sapiens | Tyrosine-protein kinase TYK2 | 6.5 | 6.5 | 6.5 | pKi | 2 |
| Homo sapiens | Vascular endothelial growth factor receptor 1 | 6.1 | 6.1 | 6.1 | pKi | 1 |
| Homo sapiens | Vascular endothelial growth factor receptor 2 | 6.4 | 6.4 | 6.4 | pKi | 1 |
| Homo sapiens | Vascular endothelial growth factor receptor 3 | 6.6 | 6.6 | 6.6 | pKi | 1 |