FAIRMol

Z56853873

Pose ID 8763 Compound 909 Pose 633

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 Z56853873
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 high Native strong SASA done
Strain ΔE
17.9 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.58, Jaccard 0.46, H-bond role recall 0.29
Burial
78%
Hydrophobic fit
71%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.982 kcal/mol/HA) ✓ Good fit quality (FQ -9.27) ✓ Good H-bonds (5 bonds) ✓ Deep burial (78% SASA buried) ✓ Lipophilic contacts well-matched (71%) ✗ Moderate strain (17.9 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-27.498
kcal/mol
LE
-0.982
kcal/mol/HA
Fit Quality
-9.27
FQ (Leeson)
HAC
28
heavy atoms
MW
417
Da
LogP
2.68
cLogP
Strain ΔE
17.9 kcal/mol
SASA buried
78%
Lipo contact
71% BSA apolar/total
SASA unbound
619 Ų
Apolar buried
342 Ų

Interaction summary

HB 5 HY 4 PI 3 CLASH 1

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 rank2.034Score-27.498
Inter norm-0.997Intra norm0.015
Top1000noExcludedno
Contacts16H-bonds5
Artifact reasongeometry warning; 8 clashes; 1 protein clash
Residues
ALA67 ARG154 ARG277 ASP158 GLU274 GLY199 GLY235 GLY236 GLY237 GLY276 HIS197 LYS69 PHE170 SER200 TYR389 VAL198

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 overlap11Native recall0.58
Jaccard0.46RMSD-
HB strict2Strict recall0.22
HB same residue+role2HB role recall0.29
HB same residue3HB residue recall0.43

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
621 1.4345497717291078 -1.0318 -28.9875 10 16 0 0.00 0.00 - no Open
624 1.9005361944032626 -0.963332 -23.5994 3 15 0 0.00 0.00 - no Open
633 2.034066149755648 -0.997448 -27.4985 5 16 11 0.58 0.29 - no Current
614 2.1205691892069596 -1.06766 -31.8052 5 10 0 0.00 0.00 - no Open
617 2.21543994317517 -0.943733 -25.4581 5 15 0 0.00 0.00 - no Open
636 2.2733624275643116 -0.935816 -24.4034 7 14 0 0.00 0.00 - no Open
631 2.613527185358712 -0.808865 -21.8381 2 15 1 0.05 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 -27.498kcal/mol
Ligand efficiency (LE) -0.9821kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.271
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 416.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.68
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 17.92kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 21.46kcal/mol
Minimised FF energy 3.54kcal/mol

SASA & burial

✓ computed
SASA (unbound) 618.6Ų
Total solvent-accessible surface area of free ligand
BSA total 481.1Ų
Buried surface area upon binding
BSA apolar 342.0Ų
Hydrophobic contacts buried
BSA polar 139.1Ų
Polar contacts buried
Fraction buried 77.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 71.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2516.7Ų
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 1391.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)