FAIRMol

NMT-TY0923

Pose ID 13229 Compound 1013 Pose 350

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
T20
T. brucei TR (Z-site (fragment hotspot)) T. brucei Z-site (fragment hotspot)
Ligand NMT-TY0923
PDB9IFH↗

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 high Native strong SASA done
Strain ΔE
28.7 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.62, Jaccard 0.36, H-bond role recall 1.00
Burial
64%
Hydrophobic fit
74%
Reason: no major geometry red flags detected
1 protein-contact clashes 47% of hydrophobic surface appears solvent-exposed (9/19 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.920 kcal/mol/HA) ✓ Good fit quality (FQ -8.79) ✓ Strong H-bond network (7 bonds) ✓ Good burial (64% SASA buried) ✓ Lipophilic contacts well-matched (74%) ✗ High strain energy (28.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-26.689
kcal/mol
LE
-0.920
kcal/mol/HA
Fit Quality
-8.79
FQ (Leeson)
HAC
29
heavy atoms
MW
432
Da
LogP
2.46
cLogP
Strain ΔE
28.7 kcal/mol
SASA buried
64%
Lipo contact
74% BSA apolar/total
SASA unbound
646 Ų
Apolar buried
302 Ų

Interaction summary

HB 7 HY 10 PI 2 CLASH 1 ⚠ Exposure 47%

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
47% of hydrophobic surface appears solvent-exposed (9/19 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 19 Buried (contacted) 10 Exposed 9 LogP 2.46 H-bonds 7
Exposed fragments: phenyl (6/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
Final rank4.599Score-26.689
Inter norm-0.671Intra norm-0.250
Top1000noExcludedno
Contacts11H-bonds7
Artifact reasongeometry warning; 11 clashes; 3 protein clashes; moderate strain Δ 28.7
Residues
GLU466 GLU467 HIS461 LEU399 MET400 PHE396 PRO398 PRO462 SER464 SER470 THR463

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name9IFHContacts8
PoseOpen native poseHB0
IFP residues
ASN402 GLU467 LEU399 PHE396 PRO398 SER394 SER470 THR397
Current overlap5Native recall0.62
Jaccard0.36RMSD-
HB strict1Strict recall0.50
HB same residue+role1HB role recall1.00
HB same residue1HB residue recall1.00

Protein summary

492 residues
Protein targetT20Atoms7539
Residues492Chains1
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:319; 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
A:FAD501

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
315 1.1613107551257762 -0.988746 -29.6316 12 16 0 0.00 0.00 - no Open
321 1.5566859020986727 -0.807286 -27.8281 8 19 0 0.00 0.00 - no Open
289 1.7875256004417812 -1.01576 -34.0347 10 17 0 0.00 0.00 - no Open
303 1.9342035494482892 -1.16396 -39.3269 9 13 0 0.00 0.00 - no Open
334 2.6091504176910982 -0.826197 -26.015 10 18 0 0.00 0.00 - no Open
367 3.0749634020371825 -0.990903 -25.5451 4 19 0 0.00 0.00 - no Open
438 3.445947979401607 -0.914081 -26.2321 6 18 0 0.00 0.00 - no Open
371 3.468473637160046 -0.952937 -25.382 5 17 0 0.00 0.00 - no Open
320 3.511127472097206 -0.833155 -22.5447 5 15 0 0.00 0.00 - no Open
407 3.597340957942763 -0.84589 -24.7448 9 14 0 0.00 0.00 - no Open
279 3.925792386612066 -1.17176 -34.1016 10 22 0 0.00 0.00 - no Open
286 4.0643906114359885 -0.970755 -26.4205 11 14 0 0.00 0.00 - no Open
307 4.098407011813724 -1.05234 -31.7217 5 14 0 0.00 0.00 - no Open
350 4.5986329465174585 -0.670614 -26.6886 7 11 5 0.62 1.00 - no Current
363 4.930702432756965 -0.921212 -24.8139 11 18 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 -26.689kcal/mol
Ligand efficiency (LE) -0.9203kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.785
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 29HA

Physicochemical properties
Molecular weight 431.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.46
Lipinski: ≤ 5
Rotatable bonds 10

Conformational strain (MMFF94s)
Strain energy (ΔE) 28.67kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -63.65kcal/mol
Minimised FF energy -92.32kcal/mol

SASA & burial

✓ computed
SASA (unbound) 646.3Ų
Total solvent-accessible surface area of free ligand
BSA total 410.5Ų
Buried surface area upon binding
BSA apolar 302.2Ų
Hydrophobic contacts buried
BSA polar 108.3Ų
Polar contacts buried
Fraction buried 63.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 73.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3084.0Ų
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 4069.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1467.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)