FAIRMol

Z1213671382

Pose ID 5223 Compound 3077 Pose 482

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
T08
T. brucei PTR1 T. brucei
Ligand Z1213671382
PDB6RX6↗

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
10.3 kcal/mol
Protein clashes
3
Internal clashes
4
Native overlap
contact recall 0.53, Jaccard 0.45, H-bond role recall 0.60
Burial
91%
Hydrophobic fit
80%
Reason: no major geometry red flags detected
3 protein-contact clashes 4 intramolecular clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.591 kcal/mol/HA) ✓ Good fit quality (FQ -14.04) ✓ Strong H-bond network (10 bonds) ✓ Deep burial (91% SASA buried) ✓ Lipophilic contacts well-matched (80%) ✗ Moderate strain (10.3 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-36.585
kcal/mol
LE
-1.591
kcal/mol/HA
Fit Quality
-14.04
FQ (Leeson)
HAC
23
heavy atoms
MW
308
Da
LogP
3.05
cLogP
Strain ΔE
10.3 kcal/mol
SASA buried
91%
Lipo contact
80% BSA apolar/total
SASA unbound
562 Ų
Apolar buried
412 Ų

Interaction summary

HB 10 HY 16 PI 2 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 rank1.436Score-36.585
Inter norm-1.619Intra norm0.028
Top1000noExcludedno
Contacts13H-bonds10
Artifact reasongeometry warning; 9 clashes; 1 protein clash; 4 cofactor-context clashes
Residues
ARG14 ASP161 CYS168 LEU208 LEU209 LYS13 LYS178 MET163 NAP301 PHE97 PRO210 TYR174 VAL211

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
NameTbPTR1_cW_6RX6_ReadyContacts19
PoseOpen native poseHB0
IFP residues
ARG14 ASP161 CYS168 GLY205 LEU208 LEU209 LYS178 MET213 NAP301 PHE171 PHE97 PRO210 PRO99 SER207 SER95 TRP221 TYR174 TYR98 VAL206
Current overlap10Native recall0.53
Jaccard0.45RMSD-
HB strict4Strict recall0.67
HB same residue+role3HB role recall0.60
HB same residue3HB residue recall0.60

Protein summary

258 residues
Protein targetT08Atoms3881
Residues258Chains2
Residue summaryLEU:437; VAL:433; ALA:361; ARG:288; ILE:266; GLU:210; LYS:198; SER:198; ASN:182; THR:154; GLN:153; PHE:140; PRO:140; TYR:126; GLY:112; HIS:103

Receptor context

1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1 Excluded HETATM 0
Kept cofactors / ions
A:NAP301

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
489 1.4121139446366726 -0.950285 -18.801 5 13 0 0.00 0.00 - no Open
482 1.4360792874215622 -1.61886 -36.5852 10 13 10 0.53 0.60 - no Current
538 1.9405720166752334 -1.23671 -27.9548 7 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 -36.585kcal/mol
Ligand efficiency (LE) -1.5907kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -14.039
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 23HA

Physicochemical properties
Molecular weight 308.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.05
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 10.29kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 44.11kcal/mol
Minimised FF energy 33.82kcal/mol

SASA & burial

✓ computed
SASA (unbound) 562.4Ų
Total solvent-accessible surface area of free ligand
BSA total 514.2Ų
Buried surface area upon binding
BSA apolar 411.7Ų
Hydrophobic contacts buried
BSA polar 102.5Ų
Polar contacts buried
Fraction buried 91.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 80.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1572.0Ų
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 2051.9Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 936.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)