FAIRMol

NMT-TY0625

Pose ID 9140 Compound 587 Pose 332

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
T14
T. brucei ODC (G418 binding site) T. brucei G418 binding site
Ligand NMT-TY0625
PDB1NJJ↗

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
35.5 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.67, Jaccard 0.50, H-bond role recall 0.60
Burial
75%
Hydrophobic fit
72%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes 65% of hydrophobic surface is solvent-exposed (11/17 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.924 kcal/mol/HA) ✓ Good fit quality (FQ -8.62) ✓ Strong H-bond network (10 bonds) ✓ Deep burial (75% SASA buried) ✓ Lipophilic contacts well-matched (72%) ✗ Very high strain energy (35.5 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-24.961
kcal/mol
LE
-0.924
kcal/mol/HA
Fit Quality
-8.62
FQ (Leeson)
HAC
27
heavy atoms
MW
403
Da
LogP
2.27
cLogP
Strain ΔE
35.5 kcal/mol
SASA buried
75%
Lipo contact
72% BSA apolar/total
SASA unbound
621 Ų
Apolar buried
337 Ų

Interaction summary

HB 10 HY 5 PI 0 CLASH 3 ⚠ Exposure 64%
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
65% of hydrophobic surface is solvent-exposed (11/17 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 17 Buried (contacted) 6 Exposed 11 LogP 2.27 H-bonds 10
Exposed fragments: phenyl (4/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
Final rank4.352Score-24.961
Inter norm-0.822Intra norm-0.105
Top1000noExcludedno
Contacts15H-bonds10
Artifact reasongeometry warning; 9 clashes; 3 protein clashes; high strain Δ 35.3
Residues
ALA283 ARG22 ARG342 ASN20 ASP385 ASP44 GLN341 GLU384 LEU339 LEU382 PRO340 PRO344 SER282 THR21 THR285

Protein summary

398 residues
Protein targetT14Atoms6140
Residues398Chains1
Residue summaryVAL:592; LEU:513; LYS:484; ARG:432; PHE:420; ILE:418; ASP:349; THR:322; TYR:315; PRO:308; GLU:301; ALA:290; SER:253; GLY:217; ASN:210; GLN:170

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:ORX602

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name1NJJContacts15
PoseOpen native poseHB0
IFP residues
ARG22 ARG242 ARG337 ARG342 ASP243 ASP385 GLN341 GLU384 LEU25 LEU339 LEU382 PRO340 PRO344 SER282 THR241
Current overlap10Native recall0.67
Jaccard0.50RMSD-
HB strict3Strict recall0.50
HB same residue+role3HB role recall0.60
HB same residue3HB residue recall0.60

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 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 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 10 0.67 0.60 - no Current
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 -24.961kcal/mol
Ligand efficiency (LE) -0.9245kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.625
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) 35.47kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -55.48kcal/mol
Minimised FF energy -90.95kcal/mol

SASA & burial

✓ computed
SASA (unbound) 621.2Ų
Total solvent-accessible surface area of free ligand
BSA total 467.2Ų
Buried surface area upon binding
BSA apolar 337.4Ų
Hydrophobic contacts buried
BSA polar 129.8Ų
Polar contacts buried
Fraction buried 75.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 72.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2427.3Ų
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 3349.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1384.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)