FAIRMol

NMT-TY0625

Pose ID 5033 Compound 587 Pose 292

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
T08
T. brucei PTR1 T. brucei
Ligand NMT-TY0625
PDB6RX6↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native mixed SASA done
Strain ΔE
32.6 kcal/mol
Protein clashes
4
Internal clashes
7
Native overlap
contact recall 0.42, Jaccard 0.36, H-bond role recall 0.40
Burial
85%
Hydrophobic fit
70%
Reason: 7 internal clashes
4 protein-contact clashes 7 intramolecular clashes 35% of hydrophobic surface appears solvent-exposed (6/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.298 kcal/mol/HA) ✓ Good fit quality (FQ -12.11) ✓ Strong H-bond network (10 bonds) ✓ Deep burial (85% SASA buried) ✓ Lipophilic contacts well-matched (70%) ✗ Very high strain energy (32.6 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (7) ✗ Many internal clashes (11)
Score
-35.045
kcal/mol
LE
-1.298
kcal/mol/HA
Fit Quality
-12.11
FQ (Leeson)
HAC
27
heavy atoms
MW
403
Da
LogP
2.27
cLogP
Strain ΔE
32.6 kcal/mol
SASA buried
85%
Lipo contact
70% BSA apolar/total
SASA unbound
625 Ų
Apolar buried
376 Ų

Interaction summary

HB 10 HY 15 PI 3 CLASH 7 ⚠ Exposure 35%

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
⚠️Partial hydrophobic solvent exposure
35% of hydrophobic surface appears solvent-exposed (6/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 17 Buried (contacted) 11 Exposed 6 LogP 2.27 H-bonds 10
Exposed fragments: phenyl (6/6 atoms exposed)
Final rank1.177Score-35.045
Inter norm-1.204Intra norm-0.094
Top1000noExcludedno
Contacts11H-bonds10
Artifact reasongeometry warning; 11 clashes; 7 protein contact clashes; 4 cofactor-context clashes; high strain Δ 32.6
Residues
ALA212 ARG14 ASP161 LEU208 LEU209 LYS13 NAP301 PHE97 PRO210 TYR174 VAL211

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 overlap8Native recall0.42
Jaccard0.36RMSD-
HB strict2Strict recall0.33
HB same residue+role2HB role recall0.40
HB same residue2HB residue recall0.40

Protein summary

258 residues
Protein targetT08Atoms3881
Residues258Chains2
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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
324 0.20723889343453514 -0.951386 -23.6661 1 14 0 0.00 0.00 - no Open
275 0.9061196009967781 -1.22993 -32.9032 9 20 0 0.00 0.00 - no Open
292 1.1768621845493887 -1.20358 -35.0455 10 11 8 0.42 0.40 - no Current
291 1.218230612835466 -1.06543 -26.4823 10 13 0 0.00 0.00 - no Open
310 1.511827099897129 -0.901999 -22.8948 4 17 0 0.00 0.00 - no Open
330 1.9924960648131407 -0.979613 -23.342 4 14 0 0.00 0.00 - no Open
343 2.359267355874073 -0.89635 -23.6694 9 12 0 0.00 0.00 - no Open
426 2.4909161669113518 -0.907217 -24.1632 10 17 0 0.00 0.00 - no Open
278 2.509428388171617 -1.0319 -28.1397 6 13 0 0.00 0.00 - no Open
297 2.63967730557778 -1.25147 -33.606 12 23 0 0.00 0.00 - no Open
355 3.229453768262364 -1.09247 -22.9997 10 19 0 0.00 0.00 - no Open
311 3.2950567359488305 -0.981974 -28.1708 9 14 0 0.00 0.00 - no Open
395 3.4109746243775096 -0.855223 -23.6426 8 13 0 0.00 0.00 - no Open
350 3.483682559989441 -0.96476 -27.5634 8 19 0 0.00 0.00 - no Open
381 3.5214059746730104 -1.11325 -28.0276 6 14 0 0.00 0.00 - no Open
364 4.0288364719309 -1.09005 -30.4446 8 17 0 0.00 0.00 - no Open
272 4.1996467964885476 -1.16921 -29.9755 9 17 0 0.00 0.00 - no Open
332 4.352390042161908 -0.822496 -24.9609 10 15 0 0.00 0.00 - no Open
271 4.392965189680496 -1.27398 -34.4428 11 15 0 0.00 0.00 - no Open
330 5.564206722433145 -0.904232 -20.3369 11 17 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 -35.045kcal/mol
Ligand efficiency (LE) -1.2980kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -12.110
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 403.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.27
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 32.58kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -51.09kcal/mol
Minimised FF energy -83.67kcal/mol

SASA & burial

✓ computed
SASA (unbound) 625.2Ų
Total solvent-accessible surface area of free ligand
BSA total 533.7Ų
Buried surface area upon binding
BSA apolar 375.6Ų
Hydrophobic contacts buried
BSA polar 158.1Ų
Polar contacts buried
Fraction buried 85.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 70.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1564.2Ų
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 940.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)