FAIRMol

Z19138088

Pose ID 8496 Compound 651 Pose 366

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
T13
T. brucei ODC (Active site) T. brucei Active site
Ligand Z19138088
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
33.6 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.68, Jaccard 0.50, H-bond role recall 0.29
Burial
77%
Hydrophobic fit
74%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.810 kcal/mol/HA) ✓ Good fit quality (FQ -8.10) ✓ Strong H-bond network (11 bonds) ✓ Deep burial (77% SASA buried) ✓ Lipophilic contacts well-matched (74%) ✗ Very high strain energy (33.6 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (19)
Score
-27.527
kcal/mol
LE
-0.810
kcal/mol/HA
Fit Quality
-8.10
FQ (Leeson)
HAC
34
heavy atoms
MW
474
Da
LogP
4.20
cLogP
Strain ΔE
33.6 kcal/mol
SASA buried
77%
Lipo contact
74% BSA apolar/total
SASA unbound
722 Ų
Apolar buried
413 Ų

Interaction summary

HB 11 HY 11 PI 4 CLASH 2
Final rank4.109Score-27.527
Inter norm-0.835Intra norm0.025
Top1000noExcludedno
Contacts20H-bonds11
Artifact reasongeometry warning; 19 clashes; 2 protein clashes; high strain Δ 33.3
Residues
ALA67 ARG154 ARG277 ASN112 ASP332 CYS114 GLU274 GLY199 GLY201 GLY236 GLY237 GLY276 HIS197 LYS169 LYS69 PHE170 PRO113 PRO275 SER200 TYR389

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

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 overlap13Native recall0.68
Jaccard0.50RMSD-
HB strict3Strict recall0.33
HB same residue+role2HB role recall0.29
HB same residue2HB residue recall0.29

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
435 1.9301717756467363 -0.72761 -23.752 6 16 1 0.05 0.00 - no Open
334 2.0263869649204853 -0.930222 -27.1777 3 21 0 0.00 0.00 - no Open
395 2.0501377984473983 -0.787007 -19.7508 5 14 0 0.00 0.00 - no Open
397 2.752858282721569 -0.800489 -23.9414 10 17 0 0.00 0.00 - no Open
396 2.7601535713818413 -0.591573 -16.9942 5 14 0 0.00 0.00 - no Open
381 2.9359635508409108 -0.793642 -19.3973 6 14 0 0.00 0.00 - no Open
450 3.1523302745872246 -0.760382 -22.134 3 18 0 0.00 0.00 - no Open
379 3.2188609293194674 -0.712407 -23.9203 8 17 0 0.00 0.00 - no Open
418 3.4321465037133247 -0.816749 -26.4904 4 18 0 0.00 0.00 - no Open
407 3.5524489581677203 -0.633858 -18.4382 7 15 0 0.00 0.00 - no Open
370 3.7807067079968997 -0.979467 -27.5375 10 15 0 0.00 0.00 - no Open
493 3.8486675627744926 -0.726729 -19.7364 7 15 0 0.00 0.00 - no Open
366 4.10912935177256 -0.834923 -27.5266 11 20 13 0.68 0.29 - no Current
336 4.160825631036783 -0.993151 -30.1156 5 15 0 0.00 0.00 - no Open
464 5.0362869852581325 -0.819442 -25.2435 6 21 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 -27.527kcal/mol
Ligand efficiency (LE) -0.8096kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.101
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 34HA

Physicochemical properties
Molecular weight 474.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.20
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 33.59kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 90.91kcal/mol
Minimised FF energy 57.32kcal/mol

SASA & burial

✓ computed
SASA (unbound) 722.1Ų
Total solvent-accessible surface area of free ligand
BSA total 559.2Ų
Buried surface area upon binding
BSA apolar 413.4Ų
Hydrophobic contacts buried
BSA polar 145.8Ų
Polar contacts buried
Fraction buried 77.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 73.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2616.2Ų
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 1377.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)