FAIRMol

Z19456272

Pose ID 8580 Compound 100 Pose 450

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 Z19456272
PDB1F3T↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising SASA cached
Promising and worth follow-up
Binding strong Geometry medium Native strong SASA done
Strain ΔE
17.9 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.74, Jaccard 0.58, H-bond role recall 0.43
Burial
82%
Hydrophobic fit
66%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.905 kcal/mol/HA) ✓ Good fit quality (FQ -8.82) ✓ Strong H-bond network (9 bonds) ✓ Deep burial (82% SASA buried) ✓ Lipophilic contacts well-matched (66%) ✗ Moderate strain (17.9 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-28.054
kcal/mol
LE
-0.905
kcal/mol/HA
Fit Quality
-8.82
FQ (Leeson)
HAC
31
heavy atoms
MW
462
Da
LogP
2.78
cLogP
Strain ΔE
17.9 kcal/mol
SASA buried
82%
Lipo contact
66% BSA apolar/total
SASA unbound
650 Ų
Apolar buried
347 Ų

Interaction summary

HB 9 HY 9 PI 3 CLASH 3
Final rank3.436Score-28.054
Inter norm-1.008Intra norm0.103
Top1000noExcludedno
Contacts19H-bonds9
Artifact reasongeometry warning; 9 clashes; 2 protein clashes
Residues
ALA111 ALA67 ALA90 ARG154 ARG277 ASN112 ASP332 GLU274 GLY235 GLY236 GLY237 GLY276 HIS197 LYS69 PHE170 PRO113 SER200 TYR331 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 overlap14Native recall0.74
Jaccard0.58RMSD-
HB strict4Strict recall0.44
HB same residue+role3HB role recall0.43
HB same residue3HB residue recall0.43

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
458 0.27097943228209714 -0.811185 -19.6635 2 14 0 0.00 0.00 - no Open
513 0.9544730494110983 -0.848599 -22.718 5 16 0 0.00 0.00 - no Open
139 1.2196504051403532 -0.732121 -21.3242 5 16 1 0.05 0.00 - no Open
506 1.3741049807450607 -0.848148 -20.44 3 19 0 0.00 0.00 - no Open
114 1.8007768117229013 -0.767307 -20.1444 8 15 0 0.00 0.00 - no Open
131 1.8058017168282356 -0.940039 -24.6674 6 14 0 0.00 0.00 - no Open
117 2.0182178879377184 -0.829303 -24.0955 5 14 0 0.00 0.00 - no Open
485 2.0994881049338083 -0.856427 -22.7639 4 13 0 0.00 0.00 - no Open
105 2.2832214801183897 -0.874039 -22.0808 4 17 0 0.00 0.00 - no Open
453 2.83121549954444 -0.908661 -22.7336 12 15 0 0.00 0.00 - no Open
447 2.8591163001678837 -0.882026 -22.5359 9 16 0 0.00 0.00 - no Open
525 2.939096492500812 -0.773608 -21.4384 5 12 0 0.00 0.00 - no Open
64 2.9866007130431282 -0.949521 -25.285 13 16 0 0.00 0.00 - no Open
450 3.435617077931159 -1.00835 -28.0542 9 19 14 0.74 0.43 - no Current
91 3.5725886357035477 -0.950541 -26.1853 11 15 0 0.00 0.00 - no Open
89 3.588860201862459 -0.897555 -24.8412 10 10 0 0.00 0.00 - no Open
425 4.484716716621432 -0.989791 -28.8598 6 13 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 -28.054kcal/mol
Ligand efficiency (LE) -0.9050kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.817
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 31HA

Physicochemical properties
Molecular weight 461.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.78
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 17.95kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 24.29kcal/mol
Minimised FF energy 6.34kcal/mol

SASA & burial

✓ computed
SASA (unbound) 650.1Ų
Total solvent-accessible surface area of free ligand
BSA total 529.8Ų
Buried surface area upon binding
BSA apolar 347.1Ų
Hydrophobic contacts buried
BSA polar 182.7Ų
Polar contacts buried
Fraction buried 81.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 65.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2518.0Ų
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 1375.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)