- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.10 Å
- Oligo State
- hetero-1-1-mer
- Ligands
- 1 x U4D: 5-(trifluoromethyl)pyridin-2-one(Non-covalent)
U4D.1: 6 residues within 4Å:- Chain A: V.23, K.24, Q.25, W.26, P.61, F.63
7 PLIP interactions:7 interactions with chain A- Hydrophobic interactions: A:P.61, A:F.63
- Hydrogen bonds: A:K.24, A:K.24, A:W.26
- pi-Stacking: A:W.26, A:W.26
- 1 x T27: 4-{[4-({4-[(E)-2-cyanoethenyl]-2,6-dimethylphenyl}amino)pyrimidin-2-yl]amino}benzonitrile(Non-covalent)
T27.2: 14 residues within 4Å:- Chain A: P.97, L.102, K.103, K.105, V.108, Y.183, Y.190, F.229, W.231, L.236, H.237, P.238, Y.320
- Chain B: E.138
16 PLIP interactions:16 interactions with chain A- Hydrophobic interactions: A:P.97, A:L.102, A:K.105, A:V.108, A:Y.183, A:Y.183, A:Y.183, A:Y.190, A:Y.190, A:W.231, A:L.236, A:Y.320
- Hydrogen bonds: A:K.103, A:K.103
- Water bridges: A:I.182, A:Y.190
- 9 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)
DMS.3: 4 residues within 4Å:- Chain A: K.333, G.335, Q.336, K.514
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:K.333
DMS.4: 7 residues within 4Å:- Chain A: W.428, Y.429, Q.430, L.527, I.528, K.530, E.531
No protein-ligand interaction detected (PLIP)DMS.5: 4 residues within 4Å:- Chain A: R.450, T.475, N.476, Q.477
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:T.475, A:N.476, A:Q.477
DMS.11: 6 residues within 4Å:- Chain A: T.378, T.388
- Chain B: T.27, T.400, W.401, E.404
1 PLIP interactions:1 interactions with chain B- Salt bridges: B:E.404
DMS.12: 4 residues within 4Å:- Chain A: Q.87
- Chain B: P.55, Y.56, K.126
No protein-ligand interaction detected (PLIP)DMS.13: 8 residues within 4Å:- Chain A: I.382, V.383
- Chain B: P.25, L.26, I.31, P.133, S.134, I.135
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:N.136
DMS.14: 4 residues within 4Å:- Chain B: L.234, H.235, W.239, R.356
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:R.356, B:R.356
DMS.15: 4 residues within 4Å:- Chain B: W.24, E.399, W.402, T.403
3 PLIP interactions:3 interactions with chain B- Water bridges: B:E.399
- Salt bridges: B:E.399
- pi-Cation interactions: B:W.24
DMS.16: 4 residues within 4Å:- Chain B: N.265, Q.269, L.422, W.426
No protein-ligand interaction detected (PLIP)- 3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.6: 5 residues within 4Å:- Chain A: E.8, V.10, S.164, S.165, K.168
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:E.8
- Water bridges: A:S.164, A:S.165
EDO.7: 6 residues within 4Å:- Chain A: K.426, L.427, W.428, Y.429, Q.511, D.513
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:W.428, A:Y.429, A:Q.511, A:D.513
EDO.17: 6 residues within 4Å:- Chain B: I.31, V.35, I.132, P.133, S.134, I.142
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:I.132, B:T.139
- 1 x MG: MAGNESIUM ION(Non-covalent)
MG.8: 3 residues within 4Å:- Chain A: D.445, D.500, D.551
5 PLIP interactions:2 interactions with chain A, 3 Ligand-Water interactions- Metal complexes: A:D.445, A:D.551, H2O.1, H2O.3, H2O.3
- 3 x SO4: SULFATE ION(Non-functional Binders)
SO4.9: 6 residues within 4Å:- Chain A: R.279, Q.280, K.283, Q.336, R.358, K.514
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:Q.280, A:R.358
- Salt bridges: A:R.279, A:K.283, A:K.514
SO4.10: 6 residues within 4Å:- Chain A: M.43, R.74, K.75, Y.148, P.152, Q.153
7 PLIP interactions:7 interactions with chain A- Hydrogen bonds: A:R.74, A:Y.148, A:Q.153
- Water bridges: A:K.75, A:K.75, A:Y.148
- Salt bridges: A:K.75
SO4.18: 8 residues within 4Å:- Chain A: T.405, E.406, Y.407, W.408
- Chain B: K.331, Q.332, G.333, K.424
4 PLIP interactions:3 interactions with chain B, 1 interactions with chain A- Hydrogen bonds: B:Q.332, A:T.405
- Salt bridges: B:K.331, B:K.424
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Chopra, A. et al., Halo Library, a Tool for Rapid Identification of Ligand Binding Sites on Proteins Using Crystallographic Fragment Screening. J.Med.Chem. (2023)
- Release Date
- 2023-05-31
- Peptides
- Reverse transcriptase/ribonuclease H: A
p51 RT: B - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B
SMTL ID : 8dxg.1
HIV-1 reverse transcriptase/rilpivirine with bound fragment 5-(trifluoromethyl)pyridin-2-ol at W24 site
Reverse transcriptase/ribonuclease H
p51 RT
Related Entries With Identical Sequence
2ykm.1 | 2ykn.1 | 2zd1.1 | 2ze2.1 | 3bgr.1 | 3ig1.1 | 3irx.1 | 3is9.1 | 3qo9.1 | 3v4i.1 | 3v4i.2 | 3v6d.1 | 3v6d.2 | 3v81.1 | 3v81.2 | 4g1q.1 | 4h4m.1 | 4h4o.1 | 4i2p.1 | 4i2q.1 | 4icl.1 | 4id5.1 | 4idk.1 | 4ifv.1 | 4ify.1 | 4ig0.1 | 4ig3.1 | 4kfb.1 | 4kko.1 | 4ko0.1 more...less...4lsl.1 | 4lsn.1 | 4mfb.1 | 4o44.1 | 4o4g.1 | 4pqu.1 | 4pqu.2 | 4puo.1 | 4puo.2 | 4pwd.1 | 4pwd.2 | 4q0b.1 | 4q0b.2 | 4r5p.1 | 4r5p.2 | 4rw4.1 | 4rw6.1 | 4rw7.1 | 4rw8.1 | 4rw9.1 | 4we1.1 | 5c25.1 | 5c42.1 | 5cym.1 | 5cyq.1 | 5hbm.1 | 5ter.1 | 5tw3.1 | 5txm.1 | 5txm.2 | 5txn.1 | 5txn.2 | 5txo.1 | 5txo.2 | 5txp.1 | 5txp.2 | 5vqq.1 | 5vqr.1 | 5vqs.1 | 5vqt.1 | 5vqu.1 | 5vqv.1 | 5vqw.1 | 5vqx.1 | 5vqy.1 | 5vqz.1 | 6c0j.1 | 6c0k.1 | 6c0l.1 | 6c0n.1 | 6c0o.1 | 6c0p.1 | 6c0r.1 | 6cgf.1 | 6dtw.1 | 6dtx.1 | 6duf.1 | 6dug.1 | 6duh.1 | 6eli.1 | 6oe3.1 | 6ul5.1 | 6x47.1 | 6x49.1 | 6x4a.1 | 6x4b.1 | 6x4c.1 | 6x4d.1 | 6x4e.1 | 6x4f.1 | 7ahx.1 | 7ahx.2 | 7aid.1 | 7aid.2 | 7aif.1 | 7aif.2 | 7aig.1 | 7aig.2 | 7aii.1 | 7aii.2 | 7aij.1 | 7aij.2 | 7krc.1 | 7krd.1 | 7kre.1 | 7krf.1 | 7kwu.1 | 7lpw.1 | 7lpx.1 | 7lqu.1 | 7ot6.1 | 7ot6.2 | 7ota.1 | 7ota.2 | 7otk.1 | 7otk.2 | 7otn.1 | 7otn.2 | 7otx.1 | 7otx.2 | 7otz.1 | 7otz.2 | 7out.1 | 7out.2 | 7ozw.1 | 7p15.1 | 7snp.1 | 7snz.1 | 7so1.1 | 7so2.1 | 7so3.1 | 7so4.1 | 7so6.1 | 7taz.1 | 7u5z.1 | 7z24.1 | 7z2d.1 | 7z2g.1 | 8dx2.1 | 8dx3.1 | 8dx8.1 | 8dxb.1 | 8dxe.1 | 8dxh.1 | 8dxi.1 | 8dxj.1 | 8dxk.1 | 8dxl.1 | 8dxm.1 | 8fe8.1 | 8ffx.1 | 8stp.1 | 8stq.1 | 8str.1 | 8sts.1 | 8sts.2 | 8stt.1 | 8stt.2 | 8stu.1 | 8stv.1 | 8stv.2 | 8u69.1 | 8u6a.1 | 8u6b.1 | 8u6c.1 | 8u6d.1 | 8u6e.1 | 8u6f.1 | 8u6g.1 | 8u6h.1 | 8u6h.2 | 8u6i.1 | 8u6j.1 | 8u6k.1 | 8u6l.1 | 8u6m.1 | 8u6n.1 | 8u6o.1 | 8u6p.1 | 8u6q.1 | 8u6r.1 | 8u6s.1 | 8u6t.1 | 8vu9.1 | 8vub.1 | 8vum.1