FAIRMol

TC487

Pose ID 9072 Compound 551 Pose 264

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
T14
T. brucei ODC (G418 binding site) T. brucei G418 binding site
Ligand TC487
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 high Native strong SASA done
Strain ΔE
22.8 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.60, Jaccard 0.43, H-bond role recall 0.20
Burial
68%
Hydrophobic fit
85%
Reason: no major geometry red flags detected
2 protein-contact clashes 73% of hydrophobic surface is solvent-exposed (16/22 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 (-0.713 kcal/mol/HA) ✓ Good fit quality (FQ -6.88) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (68% SASA buried) ✓ Lipophilic contacts well-matched (85%) ✗ High strain energy (22.8 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-21.382
kcal/mol
LE
-0.713
kcal/mol/HA
Fit Quality
-6.88
FQ (Leeson)
HAC
30
heavy atoms
MW
428
Da
LogP
3.96
cLogP
Strain ΔE
22.8 kcal/mol
SASA buried
68%
Lipo contact
85% BSA apolar/total
SASA unbound
696 Ų
Apolar buried
401 Ų

Interaction summary

HB 8 HY 2 PI 0 CLASH 2 ⚠ Exposure 72%

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
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
73% of hydrophobic surface is solvent-exposed (16/22 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 22 Buried (contacted) 6 Exposed 16 LogP 3.96 H-bonds 8
Exposed fragments: phenyl (6/6 atoms exposed)phenyl (4/6 atoms exposed)phenyl (2/5 atoms exposed)aliphatic chain/group (6 atoms exposed)
Final rank2.750Score-21.382
Inter norm-0.881Intra norm0.168
Top1000noExcludedno
Contacts15H-bonds8
Artifact reasongeometry warning; 12 clashes; 1 protein clash; moderate strain Δ 22.8
Residues
ARG242 ARG337 ASP243 ASP385 ASP47 GLU384 LEU339 LEU382 LYS51 MET386 PHE383 PRO338 SER282 THR241 VAL336

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 overlap9Native recall0.60
Jaccard0.43RMSD-
HB strict0Strict recall0.00
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
231 0.6014207356700648 -1.25321 -34.8174 5 16 0 0.00 0.00 - no Open
279 0.8504988960722657 -0.894167 -21.6384 6 19 0 0.00 0.00 - no Open
236 1.3083528962839743 -1.11776 -29.9104 4 16 0 0.00 0.00 - no Open
240 1.6299506770483856 -1.36717 -33.9407 4 17 0 0.00 0.00 - no Open
220 1.907698405551547 -0.951242 -21.9792 5 12 0 0.00 0.00 - no Open
244 1.9490770946923228 -1.20293 -34.136 7 16 0 0.00 0.00 - no Open
169 1.9707547428552354 -1.00186 -25.4722 8 19 0 0.00 0.00 - no Open
180 2.5014619286579576 -1.01708 -28.624 12 21 0 0.00 0.00 - no Open
264 2.7503390295192998 -0.880821 -21.3824 8 15 9 0.60 0.20 - no Current
165 2.77418758404451 -0.994655 -25.2548 10 17 0 0.00 0.00 - no Open
364 2.8667019787780563 -0.791058 -20.2445 7 10 0 0.00 0.00 - no Open
197 2.867821243861192 -1.03605 -27.4804 4 17 0 0.00 0.00 - no Open
309 3.2254665102249094 -0.900419 -26.4298 4 19 0 0.00 0.00 - no Open
228 3.4221328759899046 -0.818918 -19.4455 6 13 0 0.00 0.00 - no Open
190 3.711702843008295 -1.02661 -29.2265 10 20 0 0.00 0.00 - no Open
336 3.838572716904155 -0.771486 -20.5454 6 13 0 0.00 0.00 - no Open
372 4.383389719759655 -0.920685 -23.3789 10 11 0 0.00 0.00 - no Open
258 4.612847442136598 -0.816328 -20.9905 6 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 -21.382kcal/mol
Ligand efficiency (LE) -0.7127kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.875
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 427.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.96
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 22.82kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 80.09kcal/mol
Minimised FF energy 57.27kcal/mol

SASA & burial

✓ computed
SASA (unbound) 695.8Ų
Total solvent-accessible surface area of free ligand
BSA total 473.4Ų
Buried surface area upon binding
BSA apolar 401.2Ų
Hydrophobic contacts buried
BSA polar 72.2Ų
Polar contacts buried
Fraction buried 68.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 84.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2528.2Ų
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 1377.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)