FAIRMol

MK213

Pose ID 4331 Compound 741 Pose 268

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
T07
T. brucei PTR1 T. brucei
Ligand MK213
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
20.8 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.79, Jaccard 0.68, H-bond role recall 0.20
Burial
86%
Hydrophobic fit
85%
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 (-1.225 kcal/mol/HA) ✓ Good fit quality (FQ -11.82) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (86% SASA buried) ✓ Lipophilic contacts well-matched (85%) ✗ High strain energy (20.8 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-36.761
kcal/mol
LE
-1.225
kcal/mol/HA
Fit Quality
-11.82
FQ (Leeson)
HAC
30
heavy atoms
MW
409
Da
LogP
3.80
cLogP
Strain ΔE
20.8 kcal/mol
SASA buried
86%
Lipo contact
85% BSA apolar/total
SASA unbound
688 Ų
Apolar buried
500 Ų

Interaction summary

HB 6 HY 24 PI 4 CLASH 1
Final rank2.258Score-36.761
Inter norm-1.348Intra norm0.122
Top1000noExcludedno
Contacts18H-bonds6
Artifact reasongeometry warning; 11 clashes; 2 protein clashes; 1 cofactor-context clash; moderate strain Δ 20.8
Residues
ALA170 ARG14 ASP161 CYS168 GLU217 GLY205 LEU208 LEU209 MET169 MET213 NAP301 PHE171 PHE97 PRO210 PRO99 TRP221 TYR174 VAL206

Protein summary

275 residues
Protein targetT07Atoms3932
Residues275Chains3
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 overlap15Native recall0.79
Jaccard0.68RMSD-
HB strict2Strict recall0.33
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

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
270 0.41464125782172895 -1.24727 -30.931 5 18 15 0.79 0.20 - no Open
254 0.6988781872574225 -1.25188 -32.2522 4 18 15 0.79 0.20 - no Open
251 0.7250052548167374 -1.13109 -29.7477 9 16 14 0.74 0.40 - no Open
261 1.0426509139693059 -1.20512 -33.9388 8 16 14 0.74 0.20 - no Open
325 1.1123859942003849 -0.870106 -23.9953 5 17 0 0.00 0.00 - no Open
284 1.2799241570993618 -0.701211 -16.1709 2 15 0 0.00 0.00 - no Open
261 2.1714771596576723 -0.876999 -24.0478 4 20 0 0.00 0.00 - no Open
242 2.173345721097384 -0.939642 -26.2628 3 17 0 0.00 0.00 - no Open
268 2.258376845222224 -1.34754 -36.7611 6 18 15 0.79 0.20 - no Current
286 2.455516370069698 -0.756571 -20.7825 5 16 0 0.00 0.00 - no Open
231 2.507441772388101 -0.993468 -27.2209 10 16 0 0.00 0.00 - no Open
388 2.646525773858347 -0.921618 -24.6948 7 9 0 0.00 0.00 - no Open
310 3.2694404438220586 -0.809948 -22.0335 6 20 0 0.00 0.00 - no Open
382 3.283984438521126 -0.790489 -19.8104 10 13 0 0.00 0.00 - no Open
207 3.3094615427951894 -1.10423 -30.2339 10 20 0 0.00 0.00 - no Open
234 3.409408458633953 -1.09234 -29.4077 12 20 0 0.00 0.00 - no Open
245 3.4162752319055487 -0.920939 -25.2102 5 18 0 0.00 0.00 - no Open
310 3.5161728665857086 -0.795591 -22.0764 7 13 0 0.00 0.00 - no Open
391 3.596788774445806 -0.962215 -24.9581 7 10 0 0.00 0.00 - no Open
187 3.6651296797272988 -1.08872 -28.1762 10 20 0 0.00 0.00 - no Open
308 3.819364771089957 -0.792144 -21.3443 5 18 0 0.00 0.00 - no Open
264 3.966830308384504 -0.853893 -24.9405 6 14 0 0.00 0.00 - no Open
286 4.439393815944125 -0.990465 -24.6013 12 19 0 0.00 0.00 - no Open
283 4.505496780270578 -0.967133 -27.3864 10 16 0 0.00 0.00 - no Open
290 4.658138957438228 -0.76781 -20.3267 6 18 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 -36.761kcal/mol
Ligand efficiency (LE) -1.2254kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.820
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 409.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.80
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 20.83kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 56.42kcal/mol
Minimised FF energy 35.58kcal/mol

SASA & burial

✓ computed
SASA (unbound) 687.7Ų
Total solvent-accessible surface area of free ligand
BSA total 590.2Ų
Buried surface area upon binding
BSA apolar 499.9Ų
Hydrophobic contacts buried
BSA polar 90.4Ų
Polar contacts buried
Fraction buried 85.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 84.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1698.4Ų
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 929.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)