FAIRMol

NMT-TY0555

Pose ID 4357 Compound 515 Pose 294

DB SELECTIONDocking pose analysis is being read from this database.
Compound detail Protein structures Back to compounds
Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
T07
T. brucei PTR1 T. brucei
Ligand NMT-TY0555
PDB6RX6↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Weak or marginal quality
Binding strong Geometry medium Native strong SASA done
Strain ΔE
29.2 kcal/mol
Protein clashes
3
Internal clashes
4
Native overlap
contact recall 0.74, Jaccard 0.70, H-bond role recall 0.80
Burial
94%
Hydrophobic fit
66%
Reason: no major geometry red flags detected
3 protein-contact clashes 4 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.452 kcal/mol/HA) ✓ Good fit quality (FQ -12.15) ✓ Strong H-bond network (10 bonds) ✓ Deep burial (94% SASA buried) ✓ Lipophilic contacts well-matched (66%) ✗ High strain energy (29.2 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-29.042
kcal/mol
LE
-1.452
kcal/mol/HA
Fit Quality
-12.15
FQ (Leeson)
HAC
20
heavy atoms
MW
296
Da
LogP
-0.68
cLogP
Strain ΔE
29.2 kcal/mol
SASA buried
94%
Lipo contact
66% BSA apolar/total
SASA unbound
483 Ų
Apolar buried
300 Ų

Interaction summary

HB 10 HY 16 PI 4 CLASH 4
Final rank1.437Score-29.042
Inter norm-1.586Intra norm0.134
Top1000noExcludedno
Contacts15H-bonds10
Artifact reasongeometry warning; 8 clashes; 1 protein clash; 1 severe cofactor-context clash; moderate strain Δ 29.2
Residues
ALA96 ARG14 ASP161 CYS168 LEU208 LEU209 MET213 NAP301 PHE171 PHE97 PRO210 SER207 SER95 TRP221 TYR174

Protein summary

275 residues
Protein targetT07Atoms3932
Residues275Chains3
Residue summaryLEU:437; VAL:433; ALA:361; ARG:288; ILE:266; GLU:210; LYS:198; SER:198; ASN:182; THR:154; GLN:153; PHE:140; PRO:140; TYR:126; GLY:112; HIS:103

Receptor context

1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1 Excluded HETATM 0
Kept cofactors / ions
A:NAP301

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
NameTbPTR1_cW_6RX6_ReadyContacts19
PoseOpen native poseHB0
IFP residues
ARG14 ASP161 CYS168 GLY205 LEU208 LEU209 LYS178 MET213 NAP301 PHE171 PHE97 PRO210 PRO99 SER207 SER95 TRP221 TYR174 TYR98 VAL206
Current overlap14Native recall0.74
Jaccard0.70RMSD-
HB strict5Strict recall0.83
HB same residue+role4HB role recall0.80
HB same residue4HB residue recall0.80

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
291 1.1342832901296953 -1.47243 -28.1213 7 13 0 0.00 0.00 - no Open
308 1.1407956598243199 -1.47271 -28.0966 7 13 0 0.00 0.00 - no Open
287 1.425854450107728 -1.57638 -29.017 10 15 14 0.74 0.80 - no Open
294 1.4368563653499584 -1.58614 -29.0417 10 15 14 0.74 0.80 - no Current
340 1.5199875327590986 -1.30421 -24.1616 12 16 0 0.00 0.00 - no Open
325 1.8929444358902847 -1.09972 -20.59 10 11 0 0.00 0.00 - no Open
264 2.0213778030470935 -1.28263 -24.1424 8 15 0 0.00 0.00 - no Open
272 2.07930378903586 -1.19931 -21.6886 10 17 0 0.00 0.00 - no Open
288 2.272686469792997 -1.20072 -21.8379 10 17 0 0.00 0.00 - no Open
255 2.604134178216891 -1.55444 -29.5672 11 18 0 0.00 0.00 - no Open
395 2.618228131873109 -1.34198 -25.4179 10 16 0 0.00 0.00 - no Open
307 2.6395815071657873 -1.216 -22.6881 12 17 0 0.00 0.00 - no Open
324 2.719858307570968 -0.962258 -19.339 7 11 0 0.00 0.00 - no Open
272 2.890185804928903 -1.24872 -23.3539 7 15 0 0.00 0.00 - no Open
354 2.894301988851109 -1.46517 -27.278 13 19 0 0.00 0.00 - no Open
248 2.9955573621189955 -1.44392 -27.8137 14 18 0 0.00 0.00 - no Open
346 3.086475756889026 -1.42333 -26.6003 13 19 0 0.00 0.00 - no Open
299 3.1992481359795537 -1.24642 -23.7166 13 17 0 0.00 0.00 - no Open
285 3.2187089349618714 -1.29682 -23.427 10 17 0 0.00 0.00 - no Open
379 3.2560466957189305 -1.35838 -25.6607 9 16 0 0.00 0.00 - no Open
369 3.4560880962334983 -1.32647 -25.5936 9 16 0 0.00 0.00 - no Open
254 3.4642926757389616 -1.30203 -24.5606 9 15 0 0.00 0.00 - no Open
406 3.67636034041161 -1.29246 -24.4616 10 16 0 0.00 0.00 - no Open
333 3.717795610400825 -1.4146 -26.5109 10 14 0 0.00 0.00 - no Open
241 3.724783035797209 -1.26416 -21.7498 15 13 0 0.00 0.00 - no Open
251 3.7829044977730146 -1.35705 -25.1409 11 19 0 0.00 0.00 - no Open
330 3.7929991462566486 -0.942708 -18.8834 6 11 0 0.00 0.00 - no Open
241 4.010694369049239 -1.38136 -25.2742 11 19 0 0.00 0.00 - no Open
226 4.299065349056032 -1.39557 -26.9943 14 15 0 0.00 0.00 - no Open
257 4.359761779337785 -1.65662 -30.294 16 22 0 0.00 0.00 - no Open
274 4.532558280468934 -1.63443 -31.073 16 21 0 0.00 0.00 - no Open

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -29.042kcal/mol
Ligand efficiency (LE) -1.4521kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -12.151
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 20HA

Physicochemical properties
Molecular weight 296.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) -0.68
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 29.17kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -86.67kcal/mol
Minimised FF energy -115.85kcal/mol

SASA & burial

✓ computed
SASA (unbound) 482.8Ų
Total solvent-accessible surface area of free ligand
BSA total 452.2Ų
Buried surface area upon binding
BSA apolar 299.5Ų
Hydrophobic contacts buried
BSA polar 152.7Ų
Polar contacts buried
Fraction buried 93.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 66.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1465.9Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA 2051.9Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 912.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)