FAIRMol

Z275023564

Pose ID 8558 Compound 3947 Pose 428

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
T13
T. brucei ODC (Active site) T. brucei Active site
Ligand Z275023564
PDB1F3T↗

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
38.8 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.95, Jaccard 0.86, H-bond role recall 0.86
Burial
75%
Hydrophobic fit
70%
Reason: no major geometry red flags detected
5 protein-contact clashes 5 intramolecular clashes 67% of hydrophobic surface is solvent-exposed (14/21 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 (-1.596 kcal/mol/HA) ✓ Good fit quality (FQ -15.39) ✓ Strong H-bond network (14 bonds) ✓ Deep burial (75% SASA buried) ✓ Lipophilic contacts well-matched (70%) ✗ Very high strain energy (38.8 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)
Score
-47.873
kcal/mol
LE
-1.596
kcal/mol/HA
Fit Quality
-15.39
FQ (Leeson)
HAC
30
heavy atoms
MW
450
Da
LogP
3.59
cLogP
Strain ΔE
38.8 kcal/mol
SASA buried
75%
Lipo contact
70% BSA apolar/total
SASA unbound
710 Ų
Apolar buried
375 Ų

Interaction summary

HB 14 HY 3 PI 1 CLASH 5 ⚠ Exposure 66%

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
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
67% of hydrophobic surface is solvent-exposed (14/21 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 21 Buried (contacted) 7 Exposed 14 LogP 3.59 H-bonds 14
Exposed fragments: phenyl (4/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (6 atoms exposed)
Final rank5.960Score-47.873
Inter norm-0.989Intra norm-0.607
Top1000noExcludedno
Contacts20H-bonds14
Artifact reasongeometry warning; 10 clashes; 3 protein clashes; very favorable intra outlier; high strain Δ 38.8
Residues
ALA111 ALA67 ARG154 ARG277 ASP332 ASP88 CYS70 GLU274 GLY199 GLY236 GLY237 GLY276 HIS197 HIS333 LYS69 PHE238 PRO275 SER200 TYR331 TYR389

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name1F3TContacts19
PoseOpen native poseHB0
IFP residues
ALA111 ALA67 ARG154 ARG277 ASP332 ASP88 CYS70 GLU274 GLY236 GLY237 GLY276 HIS197 LYS69 PHE238 PRO275 SER200 TYR278 TYR331 TYR389
Current overlap18Native recall0.95
Jaccard0.86RMSD-
HB strict8Strict recall0.89
HB same residue+role6HB role recall0.86
HB same residue6HB residue recall0.86

Protein summary

411 residues
Protein targetT13Atoms6340
Residues411Chains1
Residue summaryVAL:624; LEU:551; LYS:506; ARG:480; PHE:460; ILE:418; ASP:348; GLU:332; THR:322; TYR:315; PRO:308; ALA:290; SER:264; GLY:224; ASN:210; GLN:170

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
486 2.7115720604137916 -0.785451 -43.2488 7 18 0 0.00 0.00 - no Open
426 4.648533217728999 -0.918232 -43.5529 10 18 0 0.00 0.00 - no Open
428 5.959795254437822 -0.989066 -47.8733 14 20 18 0.95 0.86 - no Current

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -47.873kcal/mol
Ligand efficiency (LE) -1.5958kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -15.393
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 449.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.59
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 38.84kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -19.72kcal/mol
Minimised FF energy -58.56kcal/mol

SASA & burial

✓ computed
SASA (unbound) 709.9Ų
Total solvent-accessible surface area of free ligand
BSA total 534.8Ų
Buried surface area upon binding
BSA apolar 375.4Ų
Hydrophobic contacts buried
BSA polar 159.4Ų
Polar contacts buried
Fraction buried 75.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 70.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2612.2Ų
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 3461.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1376.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)