FAIRMol

NMT-TY0625

Pose ID 2988 Compound 587 Pose 278

DB fairmolDocking 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-TY0625
PDB7PXX↗

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
34.9 kcal/mol
Protein clashes
0
Internal clashes
2
Native overlap
contact recall 0.71, Jaccard 0.67, H-bond role recall 0.33
Burial
82%
Hydrophobic fit
68%
Reason: no major geometry red flags detected
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 ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.042 kcal/mol/HA) ✓ Good fit quality (FQ -9.72) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (82% SASA buried) ✓ Lipophilic contacts well-matched (68%) ✗ Very high strain energy (34.9 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)
Score
-28.140
kcal/mol
LE
-1.042
kcal/mol/HA
Fit Quality
-9.72
FQ (Leeson)
HAC
27
heavy atoms
MW
403
Da
LogP
2.27
cLogP
Strain ΔE
34.9 kcal/mol
SASA buried
82%
Lipo contact
68% BSA apolar/total
SASA unbound
642 Ų
Apolar buried
357 Ų

Interaction summary

HB 6 HY 13 PI 3 CLASH 2 ⚠ 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 6
Exposed fragments: phenyl (6/6 atoms exposed)
Final rank2.509Score-28.140
Inter norm-1.032Intra norm-0.010
Top1000noExcludedno
Contacts13H-bonds6
Artifact reasongeometry warning; 10 clashes; 2 protein clashes; 2 cofactor-context clashes; high strain Δ 34.9
Residues
ARG17 GLY225 HIS241 LEU188 LEU226 LEU229 MET183 MET233 NDP302 PHE113 SER227 TYR194 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 overlap12Native recall0.71
Jaccard0.67RMSD-
HB strict1Strict recall0.14
HB same residue+role2HB role recall0.33
HB same residue3HB residue recall0.60

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
324 0.20723889343453514 -0.951386 -23.6661 1 14 13 0.76 0.17 - 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 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 12 0.71 0.33 - no Current
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 -28.140kcal/mol
Ligand efficiency (LE) -1.0422kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.723
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) 34.91kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -57.30kcal/mol
Minimised FF energy -92.21kcal/mol

SASA & burial

✓ computed
SASA (unbound) 641.6Ų
Total solvent-accessible surface area of free ligand
BSA total 523.5Ų
Buried surface area upon binding
BSA apolar 356.5Ų
Hydrophobic contacts buried
BSA polar 166.9Ų
Polar contacts buried
Fraction buried 81.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 68.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1618.6Ų
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 1031.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)