Table 3.
Interactions between XMRV PR and the inhibitors
| a) Hydrophobic interactions within 4.5 Å. | |||
|---|---|---|---|
| Subsite | TL-3 | Pepstatin A | Amprenavir |
| P4 | Gln36, His37, Ala52, Trp65 | Gln36, His37, Ala52, Trp53, Gln55, Trp65, Leu83 | |
| P3 | Gln36, Tyr90’ | Gln36, Gln55, Val54, Tyr90’ | |
| P2 | Ala35, Val39, Val54 | Gly34, Ala35, Gln55, His37,Val54, Gln36, Ala57’ | Ala35, Gln36, His37, Val39, Val54, Leu92 |
| P1 | Ala57, Gly56, Pro80’, Tyr90’ | Asp32, Gly34, Gln55, Gly56, Ala57, Leu30’, Asp32’, Leu92’, Cys88’, Pro89’ | Val54Gly34, Gln55, Gly56, Ala 57, Cys88’, Pro89’ Tyr90’ |
| P1’ | Gln55’, Gly56’, Ala57’, Cys88, Pro89, Tyr90, Leu92 | Asp32, Cys88, Pro89, Leu92, Gly56’, Ala57’ | Leu30, Asp32, Cys88, Pro89, Tyr90, Leu92, Gly34’, Gln55’, Gly56’, Ala57’ |
| P2’ | Gly34’, Ala35’ ,Val39’, Val54’, Gln55’, Leu83’, Leu92’ | Ala57, Gly34’, Ala35’, Gln36’, His37’, Gln55’, Gly56’, Ala57’, Leu92’ | Ala57, Ala35’, Gln36’, His37’, Val39’, Val54’, Gln55’, Leu83’, Leu92’ |
| P3’ | Gln36’, Gln55’, Tyr90 | Pro89, Tyr90, Gln36’,Trp53’, Val54’, Gln55’, | |
| P4’ | Gln36’, Gln37’, Ala52’, Trp65’ | Gln36’, His37’, Ala52’, Trp53’, Trp65’, Leu83’ | |
| b) Hydrogen bonds with TL-3 | ||
|---|---|---|
| TL-3 | XMRV PR/ Waters | Distance (Å) |
| O8 | N Gln55 | 2.90 |
| O9 | OE1 Gln36 | 3.28 |
| N4 | OE1 Gln36 , Wat53 | 3.11, 3.39 |
| O4 | N Gln36 | 2.88 |
| N2 | O Gln55 | 2.95 |
| O2 | Wat3 | 2.80 |
| N1 | O Gly34 | 2.92 |
| O1 | OD1 Asp32’, | 2.96 |
| O51 | OD1 Asp32, Asp32’ | 2.54, 2.76 |
| O51 | OD2 Asp32, Asp32’ | 3.07, 3.33 |
| N51 | O Gly34’ | 2.95 |
| O52 | Wat3 | 2.70 |
| N52 | GLn55’ | 2.86 |
| O54 | N Gln36’, Wat16 | 2.99, 3.24 |
| N54 | OE1 Gln36’ | 3.11 |
| O58 | N Gln55’ | 2.82 |
| O59 | OE1 Gln36’ | 3.18 |
| c) Hydrogen bonds with pepstatin A. The two pepstatin molecules are labeled M and J. | ||
|---|---|---|
| Pepstatin A | XMRV PR/ Waters | Distance (Å) |
| O Iva1(M) | Wat160 | 2.72 |
| N Val 2(M) | O Gly34 | 3.30 |
| O Val2(M) | N Gln36 | 2.88 |
| N Val3(M) | O Gln55 | 2.99 |
| O Val3(M) | N Gln55 | 2.86 |
| O Sta4 (M) | OE1 Gln36 | 2.94 |
| OH Sta4(M) | O Trp53 | 3.24 |
| N Sta4(M) | OE1 Gln36 | 2.96 |
| O Iva1(J) | Wat160 | 2.69 |
| N Val2(J) | O Gly34’ | 3.04 |
| O Val2(J) | N Gln36’, Wat120 | 2.88, 3.12 |
| N Val3(J) | O Gln55’ | 2.87 |
| O Val3(J) | N Gln55’ | 2.82 |
| OH Sta4(J) | O Trp53’ | 2.68 |
| N Sta4(j) | OE1 Gln36’ | 2.91 |
| d) Hydrogen bonds with amprenavir | ||
|---|---|---|
| Amprenavir | XMRV PR/Waters | Distance (Å) |
| O5, O4 | Wat10 | 2.54, 3.42 |
| N3 | O His37’ | 3.24 |
| O3 | OD1, OD2 Asp32 | 2.66, 3.21 |
| O3 | OD1, OD2 Asp32’ | 2.80, 2.89 |
| N1 | O GLy34 | 3.11 |
| O2 | Wat10 | 2.84 |
| O1 | Wat36 | 3.02 |
| O6 | N His37 | 3.45 |