6AOC
Crystal Structure of an N-Hydroxythienopyrimidine-2,4-dione RNase H Active Site Inhibitor with Multiple Binding Modes to HIV Reverse Transcriptase
Functional Information from GO Data
Chain | GOid | namespace | contents |
A | 0003676 | molecular_function | nucleic acid binding |
A | 0003964 | molecular_function | RNA-directed DNA polymerase activity |
A | 0004523 | molecular_function | RNA-DNA hybrid ribonuclease activity |
A | 0006278 | biological_process | RNA-templated DNA biosynthetic process |
B | 0003964 | molecular_function | RNA-directed DNA polymerase activity |
B | 0006278 | biological_process | RNA-templated DNA biosynthetic process |
C | 0003676 | molecular_function | nucleic acid binding |
C | 0003964 | molecular_function | RNA-directed DNA polymerase activity |
C | 0004523 | molecular_function | RNA-DNA hybrid ribonuclease activity |
C | 0006278 | biological_process | RNA-templated DNA biosynthetic process |
D | 0003964 | molecular_function | RNA-directed DNA polymerase activity |
D | 0006278 | biological_process | RNA-templated DNA biosynthetic process |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 4 |
Details | binding site for residue MN A 601 |
Chain | Residue |
A | ASP443 |
A | GLU478 |
A | ASP498 |
A | ZW2603 |
site_id | AC2 |
Number of Residues | 5 |
Details | binding site for residue MN A 602 |
Chain | Residue |
A | ASP443 |
A | ASP549 |
A | ZW2603 |
A | HOH777 |
A | HOH783 |
site_id | AC3 |
Number of Residues | 11 |
Details | binding site for residue ZW2 A 603 |
Chain | Residue |
A | ASP443 |
A | GLU478 |
A | ASP498 |
A | HIS539 |
A | ASP549 |
A | MN601 |
A | MN602 |
A | HOH730 |
A | HOH742 |
A | HOH777 |
A | HOH783 |
site_id | AC4 |
Number of Residues | 4 |
Details | binding site for residue PGE A 604 |
Chain | Residue |
A | GLN394 |
A | LYS395 |
A | GLU396 |
A | PHE416 |
site_id | AC5 |
Number of Residues | 3 |
Details | binding site for residue EDO A 605 |
Chain | Residue |
A | PHE389 |
A | GLU413 |
A | GLU415 |
site_id | AC6 |
Number of Residues | 7 |
Details | binding site for residue EDO A 606 |
Chain | Residue |
A | LYS101 |
A | LYS102 |
A | LYS103 |
A | VAL106 |
A | TYR188 |
A | PRO236 |
A | TYR318 |
site_id | AC7 |
Number of Residues | 3 |
Details | binding site for residue EDO A 607 |
Chain | Residue |
A | LYS461 |
A | ARG463 |
C | PRO468 |
site_id | AC8 |
Number of Residues | 3 |
Details | binding site for residue EDO A 608 |
Chain | Residue |
A | LYS281 |
A | ARG284 |
C | LYS70 |
site_id | AC9 |
Number of Residues | 3 |
Details | binding site for residue EDO A 609 |
Chain | Residue |
A | GLN373 |
A | THR377 |
A | HOH739 |
site_id | AD1 |
Number of Residues | 5 |
Details | binding site for residue EDO A 610 |
Chain | Residue |
A | THR403 |
A | GLU404 |
A | TYR405 |
B | LYS331 |
B | LYS424 |
site_id | AD2 |
Number of Residues | 8 |
Details | binding site for residue EDO A 611 |
Chain | Residue |
A | ALA437 |
A | GLU438 |
A | ASN460 |
A | LYS461 |
A | HOH710 |
A | HOH751 |
A | HOH765 |
B | ALA288 |
site_id | AD3 |
Number of Residues | 5 |
Details | binding site for residue EDO A 612 |
Chain | Residue |
A | ARG448 |
A | THR473 |
A | ASN474 |
A | GLN475 |
C | LYS49 |
site_id | AD4 |
Number of Residues | 6 |
Details | binding site for residue EDO A 613 |
Chain | Residue |
A | LYS476 |
A | SER515 |
A | GLU516 |
A | LEU517 |
A | HOH753 |
A | HOH848 |
site_id | AD5 |
Number of Residues | 5 |
Details | binding site for residue EDO A 614 |
Chain | Residue |
A | GLY541 |
A | GLY543 |
A | GLU546 |
A | HOH764 |
B | ARG284 |
site_id | AD6 |
Number of Residues | 3 |
Details | binding site for residue EDO A 615 |
Chain | Residue |
A | GLN547 |
A | LYS550 |
A | LEU551 |
site_id | AD7 |
Number of Residues | 6 |
Details | binding site for residue EDO A 616 |
Chain | Residue |
A | TYR339 |
A | GLN340 |
A | GLY352 |
A | EDO617 |
A | HOH748 |
A | HOH920 |
site_id | AD8 |
Number of Residues | 2 |
Details | binding site for residue EDO A 617 |
Chain | Residue |
A | GLN330 |
A | EDO616 |
site_id | AD9 |
Number of Residues | 8 |
Details | binding site for residue EDO A 618 |
Chain | Residue |
A | LYS331 |
A | GLY333 |
A | GLN334 |
A | GLY335 |
A | ARG356 |
A | ASP364 |
A | GLN367 |
A | HOH744 |
site_id | AE1 |
Number of Residues | 9 |
Details | binding site for residue PGE B 501 |
Chain | Residue |
B | HOH739 |
B | VAL75 |
B | PHE77 |
B | ASN81 |
B | GLY152 |
B | TYR183 |
B | THR386 |
B | TRP410 |
B | ILE411 |
site_id | AE2 |
Number of Residues | 12 |
Details | binding site for residue PGE B 502 |
Chain | Residue |
B | LYS30 |
B | ILE63 |
B | LYS64 |
B | LYS65 |
B | LYS66 |
B | ASP67 |
B | THR403 |
B | GLU404 |
B | TRP406 |
B | GLN407 |
B | EDO520 |
D | HOH693 |
site_id | AE3 |
Number of Residues | 11 |
Details | binding site for residue PGE B 503 |
Chain | Residue |
B | LYS65 |
B | LYS66 |
B | TYR188 |
B | TYR232 |
B | THR377 |
B | GLN407 |
B | ALA408 |
B | TRP410 |
B | EDO507 |
B | EDO509 |
B | HOH781 |
site_id | AE4 |
Number of Residues | 12 |
Details | binding site for residue PGE B 504 |
Chain | Residue |
A | GLU194 |
A | HOH961 |
B | ILE94 |
B | PRO95 |
B | PRO97 |
B | LYS172 |
B | ILE180 |
B | TYR181 |
B | GLN182 |
B | HOH666 |
B | HOH772 |
B | HOH847 |
site_id | AE5 |
Number of Residues | 5 |
Details | binding site for residue EDO B 505 |
Chain | Residue |
B | TRP24 |
B | GLU399 |
B | TRP402 |
B | EDO506 |
B | HOH678 |
site_id | AE6 |
Number of Residues | 8 |
Details | binding site for residue EDO B 506 |
Chain | Residue |
B | TRP24 |
B | ARG78 |
B | GLU399 |
B | TRP414 |
B | EDO505 |
B | HOH634 |
B | HOH720 |
B | HOH741 |
site_id | AE7 |
Number of Residues | 7 |
Details | binding site for residue EDO B 507 |
Chain | Residue |
B | LYS66 |
B | TYR232 |
B | GLU370 |
B | GLN373 |
B | THR377 |
B | PGE503 |
B | EDO508 |
site_id | AE8 |
Number of Residues | 4 |
Details | binding site for residue EDO B 508 |
Chain | Residue |
B | TRP239 |
B | LYS374 |
B | GLU378 |
B | EDO507 |
site_id | AE9 |
Number of Residues | 6 |
Details | binding site for residue EDO B 509 |
Chain | Residue |
B | LYS65 |
B | VAL108 |
B | ASP110 |
B | ASP186 |
B | TYR232 |
B | PGE503 |
site_id | AF1 |
Number of Residues | 5 |
Details | binding site for residue EDO B 510 |
Chain | Residue |
B | GLU328 |
B | ILE329 |
B | GLN330 |
B | PRO392 |
B | PRO421 |
site_id | AF2 |
Number of Residues | 6 |
Details | binding site for residue EDO B 511 |
Chain | Residue |
B | GLN334 |
B | GLY335 |
B | HIS361 |
B | HOH652 |
B | HOH733 |
B | HOH779 |
site_id | AF3 |
Number of Residues | 5 |
Details | binding site for residue EDO B 512 |
Chain | Residue |
B | GLU6 |
B | VAL8 |
B | VAL118 |
B | SER162 |
B | HOH619 |
site_id | AF4 |
Number of Residues | 7 |
Details | binding site for residue EDO B 513 |
Chain | Residue |
B | PRO1 |
B | SER3 |
B | PRO119 |
B | ARG125 |
B | ASN147 |
B | HOH657 |
B | HOH770 |
site_id | AF5 |
Number of Residues | 2 |
Details | binding site for residue EDO B 514 |
Chain | Residue |
B | SER3 |
B | SER117 |
site_id | AF6 |
Number of Residues | 3 |
Details | binding site for residue EDO B 515 |
Chain | Residue |
A | GLU169 |
B | GLU42 |
B | LYS49 |
site_id | AF7 |
Number of Residues | 4 |
Details | binding site for residue EDO B 516 |
Chain | Residue |
B | ASN81 |
B | LYS154 |
B | MET184 |
B | HOH739 |
site_id | AF8 |
Number of Residues | 6 |
Details | binding site for residue EDO B 517 |
Chain | Residue |
B | ILE94 |
B | PRO157 |
B | TYR181 |
B | GLN182 |
B | TYR183 |
B | MET184 |
site_id | AF9 |
Number of Residues | 1 |
Details | binding site for residue EDO B 518 |
Chain | Residue |
B | LYS126 |
site_id | AG1 |
Number of Residues | 8 |
Details | binding site for residue EDO B 519 |
Chain | Residue |
B | PHE416 |
B | ASN418 |
B | HOH601 |
B | HOH740 |
B | HOH827 |
C | GLU28 |
C | GLU29 |
C | EDO618 |
site_id | AG2 |
Number of Residues | 8 |
Details | binding site for residue EDO B 520 |
Chain | Residue |
B | ARG358 |
B | LYS366 |
B | GLU404 |
B | TYR405 |
B | PGE502 |
B | HOH756 |
D | GLU300 |
D | HOH775 |
site_id | AG3 |
Number of Residues | 6 |
Details | binding site for residue EDO B 521 |
Chain | Residue |
B | THR27 |
B | THR400 |
B | TRP401 |
B | GLU404 |
B | EDO523 |
B | HOH631 |
site_id | AG4 |
Number of Residues | 7 |
Details | binding site for residue EDO B 522 |
Chain | Residue |
B | THR240 |
B | VAL241 |
B | GLN242 |
B | TYR339 |
B | GLY352 |
B | LYS353 |
B | HOH712 |
site_id | AG5 |
Number of Residues | 9 |
Details | binding site for residue EDO B 523 |
Chain | Residue |
B | PRO25 |
B | LEU26 |
B | THR27 |
B | LYS30 |
B | THR403 |
B | EDO521 |
B | HOH602 |
B | HOH631 |
B | HOH705 |
site_id | AG6 |
Number of Residues | 4 |
Details | binding site for residue MN C 601 |
Chain | Residue |
C | ASP443 |
C | GLU478 |
C | ASP498 |
C | ZW2603 |
site_id | AG7 |
Number of Residues | 5 |
Details | binding site for residue MN C 602 |
Chain | Residue |
C | ASP443 |
C | ASP549 |
C | ZW2603 |
C | HOH755 |
C | HOH882 |
site_id | AG8 |
Number of Residues | 10 |
Details | binding site for residue ZW2 C 603 |
Chain | Residue |
C | ASP443 |
C | GLU478 |
C | ASP498 |
C | HIS539 |
C | ASP549 |
C | MN601 |
C | MN602 |
C | EDO622 |
C | EDO623 |
C | HOH882 |
site_id | AG9 |
Number of Residues | 5 |
Details | binding site for residue EDO C 604 |
Chain | Residue |
C | ASP121 |
C | GLU122 |
C | ASP123 |
C | EDO605 |
C | HOH701 |
site_id | AH1 |
Number of Residues | 6 |
Details | binding site for residue EDO C 605 |
Chain | Residue |
C | VAL10 |
C | LYS11 |
C | ASP121 |
C | ASP123 |
C | EDO604 |
C | HOH933 |
site_id | AH2 |
Number of Residues | 4 |
Details | binding site for residue EDO C 606 |
Chain | Residue |
C | LYS103 |
C | VAL106 |
C | TYR188 |
C | TYR318 |
site_id | AH3 |
Number of Residues | 3 |
Details | binding site for residue EDO C 607 |
Chain | Residue |
C | TYR183 |
C | ASP186 |
C | HOH836 |
site_id | AH4 |
Number of Residues | 2 |
Details | binding site for residue EDO C 608 |
Chain | Residue |
C | PHE346 |
C | ASN348 |
site_id | AH5 |
Number of Residues | 6 |
Details | binding site for residue EDO C 609 |
Chain | Residue |
C | THR377 |
C | ILE380 |
D | TRP24 |
D | PRO25 |
D | GLU399 |
D | PGE502 |
site_id | AH6 |
Number of Residues | 3 |
Details | binding site for residue EDO C 610 |
Chain | Residue |
C | GLN500 |
D | TRP266 |
D | HOH702 |
site_id | AH7 |
Number of Residues | 8 |
Details | binding site for residue EDO C 611 |
Chain | Residue |
C | GLY436 |
C | ALA437 |
C | GLU438 |
C | ASN460 |
C | LYS461 |
C | HOH717 |
C | HOH827 |
D | ALA288 |
site_id | AH8 |
Number of Residues | 4 |
Details | binding site for residue EDO C 612 |
Chain | Residue |
A | GLU248 |
A | LYS249 |
A | ASP250 |
C | PRO14 |
site_id | AH9 |
Number of Residues | 4 |
Details | binding site for residue EDO C 613 |
Chain | Residue |
C | PRO1 |
C | ILE2 |
C | GLY213 |
C | HOH837 |
site_id | AI1 |
Number of Residues | 1 |
Details | binding site for residue EDO C 614 |
Chain | Residue |
C | GLU6 |
site_id | AI2 |
Number of Residues | 5 |
Details | binding site for residue EDO C 615 |
Chain | Residue |
C | VAL10 |
C | LYS11 |
C | LEU12 |
C | ASP123 |
C | TYR127 |
site_id | AI3 |
Number of Residues | 5 |
Details | binding site for residue EDO C 616 |
Chain | Residue |
C | ASP17 |
C | LYS20 |
C | PRO55 |
C | TYR56 |
C | HOH945 |
site_id | AI4 |
Number of Residues | 4 |
Details | binding site for residue EDO C 617 |
Chain | Residue |
C | ASN54 |
C | PRO55 |
C | ASN57 |
C | ARG143 |
site_id | AI5 |
Number of Residues | 5 |
Details | binding site for residue EDO C 618 |
Chain | Residue |
B | LYS395 |
B | EDO519 |
B | HOH723 |
B | HOH740 |
C | GLU29 |
site_id | AI6 |
Number of Residues | 4 |
Details | binding site for residue EDO C 619 |
Chain | Residue |
C | SER48 |
C | LYS49 |
C | ILE50 |
C | HOH763 |
site_id | AI7 |
Number of Residues | 6 |
Details | binding site for residue EDO C 620 |
Chain | Residue |
C | ARG78 |
C | ASN81 |
C | LYS82 |
C | HOH704 |
C | HOH810 |
C | HOH860 |
site_id | AI8 |
Number of Residues | 4 |
Details | binding site for residue EDO C 621 |
Chain | Residue |
C | TYR115 |
C | GLY152 |
C | SER156 |
C | HOH814 |
site_id | AI9 |
Number of Residues | 5 |
Details | binding site for residue EDO C 622 |
Chain | Residue |
C | GLY444 |
C | ASN474 |
C | GLU478 |
C | ZW2603 |
C | EDO623 |
site_id | AJ1 |
Number of Residues | 6 |
Details | binding site for residue EDO C 623 |
Chain | Residue |
C | GLU478 |
C | ASP498 |
C | SER499 |
C | ZW2603 |
C | EDO622 |
C | HOH838 |
site_id | AJ2 |
Number of Residues | 8 |
Details | binding site for residue EDO C 624 |
Chain | Residue |
C | TYR427 |
C | GLN428 |
C | LEU525 |
C | LYS528 |
C | GLU529 |
C | VAL531 |
C | HOH710 |
C | HOH736 |
site_id | AJ3 |
Number of Residues | 4 |
Details | binding site for residue EDO C 625 |
Chain | Residue |
C | PRO4 |
C | ARG211 |
C | TRP212 |
C | HOH976 |
site_id | AJ4 |
Number of Residues | 3 |
Details | binding site for residue EDO C 626 |
Chain | Residue |
C | GLU89 |
C | GLN161 |
C | HOH735 |
site_id | AJ5 |
Number of Residues | 11 |
Details | binding site for residue PGE D 501 |
Chain | Residue |
D | LEU74 |
D | VAL75 |
D | PHE77 |
D | ASN81 |
D | GLY152 |
D | TYR183 |
D | MET184 |
D | THR386 |
D | TRP410 |
D | ILE411 |
D | HOH737 |
site_id | AJ6 |
Number of Residues | 10 |
Details | binding site for residue PGE D 502 |
Chain | Residue |
C | EDO609 |
D | TRP24 |
D | GLU399 |
D | THR400 |
D | TRP401 |
D | TRP402 |
D | THR403 |
D | EDO504 |
D | HOH692 |
D | HOH694 |
site_id | AJ7 |
Number of Residues | 5 |
Details | binding site for residue EDO D 503 |
Chain | Residue |
D | ILE63 |
D | LYS64 |
D | GLU404 |
D | TRP406 |
D | GLN407 |
site_id | AJ8 |
Number of Residues | 6 |
Details | binding site for residue EDO D 504 |
Chain | Residue |
D | ARG78 |
D | GLU399 |
D | TRP414 |
D | PGE502 |
D | HOH607 |
D | HOH630 |
site_id | AJ9 |
Number of Residues | 2 |
Details | binding site for residue EDO D 505 |
Chain | Residue |
D | GLN85 |
D | ASP86 |
site_id | AK1 |
Number of Residues | 3 |
Details | binding site for residue EDO D 506 |
Chain | Residue |
D | VAL241 |
D | LEU349 |
D | LYS350 |
site_id | AK2 |
Number of Residues | 7 |
Details | binding site for residue EDO D 507 |
Chain | Residue |
D | LYS65 |
D | VAL108 |
D | LEU109 |
D | ASP110 |
D | ASP186 |
D | MET230 |
D | HOH678 |
site_id | AK3 |
Number of Residues | 4 |
Details | binding site for residue EDO D 508 |
Chain | Residue |
D | THR286 |
D | LYS287 |
D | GLU291 |
D | HOH603 |
site_id | AK4 |
Number of Residues | 5 |
Details | binding site for residue EDO D 509 |
Chain | Residue |
D | GLU298 |
D | LEU301 |
D | GLU305 |
D | HOH649 |
D | HOH684 |
site_id | AK5 |
Number of Residues | 4 |
Details | binding site for residue EDO D 510 |
Chain | Residue |
D | TYR232 |
D | TRP239 |
D | LYS374 |
D | GLU378 |
site_id | AK6 |
Number of Residues | 5 |
Details | binding site for residue EDO D 511 |
Chain | Residue |
D | LYS395 |
D | GLU396 |
D | GLU399 |
D | HOH694 |
D | HOH748 |
site_id | AK7 |
Number of Residues | 4 |
Details | binding site for residue EDO D 512 |
Chain | Residue |
C | PRO433 |
D | THR253 |
D | THR290 |
D | HOH623 |
site_id | AK8 |
Number of Residues | 4 |
Details | binding site for residue EDO D 513 |
Chain | Residue |
D | TYR183 |
D | LYS385 |
D | THR386 |
D | LYS388 |
site_id | AK9 |
Number of Residues | 6 |
Details | binding site for residue EDO D 514 |
Chain | Residue |
D | GLU328 |
D | ILE329 |
D | GLN330 |
D | LYS390 |
D | VAL417 |
D | THR419 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 6 |
Details | BINDING: |
Chain | Residue | Details |
B | ASP110 | |
B | ASP185 | |
B | ASP186 | |
D | ASP110 | |
D | ASP185 | |
D | ASP186 |
site_id | SWS_FT_FI2 |
Number of Residues | 4 |
Details | SITE: Essential for RT p66/p51 heterodimerization |
Chain | Residue | Details |
B | TRP401 | |
B | TRP414 | |
D | TRP401 | |
D | TRP414 | |
C | ASP443 | |
C | GLU478 | |
C | ASP498 | |
C | ASP549 |
site_id | SWS_FT_FI3 |
Number of Residues | 4 |
Details | SITE: Essential for RT p66/p51 heterodimerization |
Chain | Residue | Details |
A | TRP401 | |
A | TRP414 | |
C | TRP401 | |
C | TRP414 |
site_id | SWS_FT_FI4 |
Number of Residues | 2 |
Details | SITE: Cleavage; by viral protease; partial |
Chain | Residue | Details |
A | PHE440 | |
C | PHE440 |