FAIRMol

NMT-TY0625

Pose ID 12476 Compound 587 Pose 275

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
T19
T. brucei TR (NADPH binding site) T. brucei NADPH binding site
Ligand NMT-TY0625
PDB2WOV↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Likely artefact or unreliable pose
Binding strong Geometry medium Native mixed SASA done
Strain ΔE
34.3 kcal/mol
Protein clashes
1
Internal clashes
3
Native overlap
contact recall 0.26, Jaccard 0.17, H-bond role recall 0.40
Burial
92%
Hydrophobic fit
72%
Reason: no major geometry red flags detected
1 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.219 kcal/mol/HA) ✓ Good fit quality (FQ -11.37) ✓ Strong H-bond network (9 bonds) ✓ Deep burial (92% SASA buried) ✓ Lipophilic contacts well-matched (72%) ✗ Very high strain energy (34.3 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (6) ✗ Internal clashes (9)
Score
-32.903
kcal/mol
LE
-1.219
kcal/mol/HA
Fit Quality
-11.37
FQ (Leeson)
HAC
27
heavy atoms
MW
403
Da
LogP
2.27
cLogP
Strain ΔE
34.3 kcal/mol
SASA buried
92%
Lipo contact
72% BSA apolar/total
SASA unbound
637 Ų
Apolar buried
424 Ų

Interaction summary

HB 9 HY 16 PI 0 CLASH 3
Final rank0.906Score-32.903
Inter norm-1.230Intra norm-0.025
Top1000noExcludedno
Contacts20H-bonds9
Artifact reasongeometry warning; 9 clashes; 6 protein contact clashes; 2 cofactor-context clashes; high strain Δ 34.3
Residues
ALA363 ALA365 ARG287 ASP327 CYS52 CYS57 GLN439 GLU436 GLY56 ILE438 LEU334 LYS60 MET333 NDP800 PHE367 PRO336 PRO435 SER364 THR335 THR51

Protein summary

493 residues
Protein targetT19Atoms7541
Residues493Chains1
Residue summaryVAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:330; TYR:294; ASP:264; MET:221

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
C:NDP800

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name2WOVContacts27
PoseOpen native poseHB0
IFP residues
ALA284 ALA365 ARG222 ARG228 ARG287 ASN223 ASN254 GLN165 GLU202 GLY195 GLY196 GLY197 GLY286 ILE199 ILE285 LEU227 LEU334 LYS60 MET333 NDP800 PHE198 PHE367 PRO167 SER200 TYR221 VAL194 VAL366
Current overlap7Native recall0.26
Jaccard0.17RMSD-
HB strict2Strict recall0.17
HB same residue+role2HB role recall0.40
HB same residue1HB residue recall0.25

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

PI · π–π interactions
No pi · π–π interactions detected for this pose.

HY · Hydrophobic contacts

CLASH · Clashes

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 7 0.26 0.40 - no Current
292 1.1768621845493887 -1.20358 -35.0455 10 11 0 0.00 0.00 - no Open
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 -32.903kcal/mol
Ligand efficiency (LE) -1.2186kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.369
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) 34.32kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -55.95kcal/mol
Minimised FF energy -90.27kcal/mol

SASA & burial

✓ computed
SASA (unbound) 636.5Ų
Total solvent-accessible surface area of free ligand
BSA total 587.5Ų
Buried surface area upon binding
BSA apolar 424.4Ų
Hydrophobic contacts buried
BSA polar 163.1Ų
Polar contacts buried
Fraction buried 92.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 72.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3049.8Ų
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 4064.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1480.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)