FAIRMol

NMT-TY0139

Pose ID 2961 Compound 1819 Pose 251

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
T05
L. major PTR1 L. major
Ligand NMT-TY0139
PDB7PXX↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising SASA cached
Promising and worth follow-up
Binding strong Geometry high Native strong SASA done
Strain ΔE
7.6 kcal/mol
Protein clashes
0
Internal clashes
2
Native overlap
contact recall 0.65, Jaccard 0.55, H-bond role recall 0.33
Burial
97%
Hydrophobic fit
47%
Reason: no major geometry red flags detected
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Low conformational strain (7.6 kcal/mol) ✓ Excellent LE (-2.047 kcal/mol/HA) ✓ Good fit quality (FQ -15.12) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (97% SASA buried) ✗ Geometry warnings
Score
-30.702
kcal/mol
LE
-2.047
kcal/mol/HA
Fit Quality
-15.12
FQ (Leeson)
HAC
15
heavy atoms
MW
225
Da
LogP
-0.85
cLogP
Strain ΔE
7.6 kcal/mol
SASA buried
97%
Lipo contact
47% BSA apolar/total
SASA unbound
375 Ų
Apolar buried
173 Ų

Interaction summary

HB 6 HY 10 PI 2 CLASH 0

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
No clash · clashes detected for this pose.
Final rank1.240Score-30.702
Inter norm-1.911Intra norm-0.136
Top1000noExcludedno
Contacts14H-bonds6
Artifact reasongeometry warning; 2 clashes; 2 protein clashes
Residues
ARG17 ASP181 HIS241 LEU188 LEU226 LEU229 MET183 NDP302 PHE113 SER227 TYR194 VAL228 VAL230 ARG287

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
NameligandContacts17
PoseOpen native poseHB0
IFP residues
ARG17 GLY225 HIS241 LEU188 LEU226 LEU229 LYS198 MET233 NDP302 PHE113 PRO115 SER111 SER227 TYR191 TYR194 VAL230 ARG287
Current overlap11Native recall0.65
Jaccard0.55RMSD-
HB strict2Strict recall0.29
HB same residue+role2HB role recall0.33
HB same residue2HB residue recall0.40

Protein summary

274 residues
Protein targetT05Atoms4108
Residues274Chains2
Residue summaryLEU:494; ALA:421; ARG:384; VAL:368; THR:295; TYR:231; SER:198; PRO:196; ILE:190; LYS:176; ASN:154; GLU:150; GLY:126; PHE:120; HIS:119; ASP:108

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:NDP302

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
283 -1.43235038960848 -2.02036 -29.0308 7 10 0 0.00 0.00 - no Open
251 1.2396203427272454 -1.91109 -30.7021 6 14 11 0.65 0.33 - no Current
276 1.5261822919367496 -1.62124 -23.3378 6 10 9 0.53 0.67 - 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 -30.702kcal/mol
Ligand efficiency (LE) -2.0468kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -15.124
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 15HA

Physicochemical properties
Molecular weight 225.2Da
Lipinski: ≤ 500 Da
LogP (cLogP) -0.85
Lipinski: ≤ 5
Rotatable bonds 2

Conformational strain (MMFF94s)
Strain energy (ΔE) 7.65kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -5.22kcal/mol
Minimised FF energy -12.87kcal/mol

SASA & burial

✓ computed
SASA (unbound) 374.5Ų
Total solvent-accessible surface area of free ligand
BSA total 364.5Ų
Buried surface area upon binding
BSA apolar 172.8Ų
Hydrophobic contacts buried
BSA polar 191.7Ų
Polar contacts buried
Fraction buried 97.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 47.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1336.1Ų
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 2179.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1021.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)