FAIRMol

NMT-TY0959

Pose ID 5054 Compound 527 Pose 313

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
T08
T. brucei PTR1 T. brucei
Ligand NMT-TY0959
PDB6RX6↗

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 high Native strong SASA done
Strain ΔE
29.9 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.74, Jaccard 0.70, H-bond role recall 0.40
Burial
88%
Hydrophobic fit
71%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.247 kcal/mol/HA) ✓ Good fit quality (FQ -11.63) ✓ Strong H-bond network (12 bonds) ✓ Deep burial (88% SASA buried) ✓ Lipophilic contacts well-matched (71%) ✗ High strain energy (29.9 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-33.660
kcal/mol
LE
-1.247
kcal/mol/HA
Fit Quality
-11.63
FQ (Leeson)
HAC
27
heavy atoms
MW
403
Da
LogP
2.44
cLogP
Strain ΔE
29.9 kcal/mol
SASA buried
88%
Lipo contact
71% BSA apolar/total
SASA unbound
622 Ų
Apolar buried
392 Ų

Interaction summary

HB 12 HY 16 PI 3 CLASH 1
Final rank1.314Score-33.660
Inter norm-1.310Intra norm0.063
Top1000noExcludedno
Contacts15H-bonds12
Artifact reasongeometry warning; 9 clashes; 1 protein clash; 1 severe cofactor-context clash; moderate strain Δ 29.8
Residues
ALA96 ARG14 ASP161 CYS168 GLY205 LEU208 LEU209 NAP301 PHE97 PRO210 SER95 TRP221 TYR174 TYR98 VAL206

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

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 overlap14Native recall0.74
Jaccard0.70RMSD-
HB strict3Strict recall0.50
HB same residue+role2HB role recall0.40
HB same residue3HB residue recall0.60

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
350 0.3629211958252925 -0.926251 -24.8853 2 13 0 0.00 0.00 - no Open
308 0.8712687604222177 -1.14475 -30.9484 7 15 14 0.74 0.40 - no Open
313 1.3142726160638258 -1.30957 -33.6603 12 15 14 0.74 0.40 - no Current
337 1.7652358533706136 -0.983958 -24.6706 6 21 0 0.00 0.00 - no Open
326 1.9773175739360493 -1.1336 -31.1195 10 21 0 0.00 0.00 - no Open
291 2.165473959343045 -1.26034 -34.3636 9 22 0 0.00 0.00 - no Open
301 2.480529293523874 -1.03512 -28.7525 9 12 0 0.00 0.00 - no Open
391 2.9008417563283935 -1.06217 -28.0759 7 15 0 0.00 0.00 - no Open
405 2.9806369013586718 -1.18262 -29.8648 6 15 0 0.00 0.00 - no Open
381 3.0321874169205607 -1.08611 -28.6887 6 16 0 0.00 0.00 - no Open
379 3.2808649478445537 -0.969429 -25.6956 10 17 0 0.00 0.00 - no Open
332 3.3588118370115048 -1.08116 -27.9486 7 17 0 0.00 0.00 - no Open
416 3.387046221950613 -0.924839 -25.7132 8 13 0 0.00 0.00 - no Open
334 3.429500560915679 -1.04914 -24.4852 8 15 0 0.00 0.00 - no Open
349 3.654496302035269 -0.850128 -21.98 8 14 0 0.00 0.00 - no Open
302 3.8731875216797746 -1.1408 -30.4082 8 22 0 0.00 0.00 - no Open
286 4.0813402406540185 -0.908062 -25.3939 13 15 0 0.00 0.00 - no Open
358 4.09740218547716 -0.710564 -18.8071 6 10 0 0.00 0.00 - no Open
336 4.132326379777683 -0.942975 -24.3804 7 17 0 0.00 0.00 - no Open
453 4.769829786717276 -1.02855 -27.026 8 17 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 -33.660kcal/mol
Ligand efficiency (LE) -1.2467kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.631
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 403.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.44
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 29.91kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -50.04kcal/mol
Minimised FF energy -79.94kcal/mol

SASA & burial

✓ computed
SASA (unbound) 622.4Ų
Total solvent-accessible surface area of free ligand
BSA total 550.2Ų
Buried surface area upon binding
BSA apolar 391.6Ų
Hydrophobic contacts buried
BSA polar 158.6Ų
Polar contacts buried
Fraction buried 88.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 71.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1574.2Ų
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 2051.9Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 936.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)