FAIRMol

Z31204537

Pose ID 8651 Compound 2037 Pose 521

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 Z31204537
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
13.1 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.63, Jaccard 0.60, H-bond role recall 0.57
Burial
74%
Hydrophobic fit
65%
Reason: no major geometry red flags detected
4 protein-contact clashes 4 intramolecular clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.327 kcal/mol/HA) ✓ Good fit quality (FQ -11.72) ✓ Strong H-bond network (11 bonds) ✓ Deep burial (74% SASA buried) ✓ Lipophilic contacts well-matched (65%) ✗ Moderate strain (13.1 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-30.532
kcal/mol
LE
-1.327
kcal/mol/HA
Fit Quality
-11.72
FQ (Leeson)
HAC
23
heavy atoms
MW
340
Da
LogP
3.44
cLogP
Strain ΔE
13.1 kcal/mol
SASA buried
74%
Lipo contact
65% BSA apolar/total
SASA unbound
521 Ų
Apolar buried
250 Ų

Interaction summary

HB 11 HY 4 PI 3 CLASH 4

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
Final rank3.387Score-30.532
Inter norm-1.223Intra norm-0.104
Top1000noExcludedno
Contacts13H-bonds11
Artifact reasongeometry warning; 8 clashes; 2 protein clashes
Residues
ALA67 ARG154 ARG277 ASP88 GLU274 GLY199 GLY236 GLY237 GLY276 HIS197 LYS69 SER200 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 overlap12Native recall0.63
Jaccard0.60RMSD-
HB strict5Strict recall0.56
HB same residue+role4HB role recall0.57
HB same residue4HB residue recall0.57

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
517 0.42060271769283386 -1.01265 -25.7013 1 17 0 0.00 0.00 - no Open
507 1.3740988223350297 -1.21271 -31.4004 3 11 0 0.00 0.00 - no Open
518 2.1812899757260524 -1.06483 -25.1728 3 11 0 0.00 0.00 - no Open
521 3.387400045559614 -1.22342 -30.5321 11 13 12 0.63 0.57 - 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 -30.532kcal/mol
Ligand efficiency (LE) -1.3275kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.716
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 23HA

Physicochemical properties
Molecular weight 340.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.44
Lipinski: ≤ 5
Rotatable bonds 3

Conformational strain (MMFF94s)
Strain energy (ΔE) 13.07kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 25.17kcal/mol
Minimised FF energy 12.10kcal/mol

SASA & burial

✓ computed
SASA (unbound) 521.3Ų
Total solvent-accessible surface area of free ligand
BSA total 384.0Ų
Buried surface area upon binding
BSA apolar 250.4Ų
Hydrophobic contacts buried
BSA polar 133.6Ų
Polar contacts buried
Fraction buried 73.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 65.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2408.8Ų
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 1393.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)